diff --git a/DESCRIPTION b/DESCRIPTION index cdcd8838..f352ce85 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: ggspectra Type: Package Title: Extensions to 'ggplot2' for Radiation Spectra Version: 0.3.14.9000 -Date: 2024-12-05 +Date: 2024-12-07 Authors@R: c( person("Pedro J.", "Aphalo", email = "pedro.aphalo@helsinki.fi", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3385-972X")), @@ -19,7 +19,7 @@ LazyLoad: TRUE ByteCompile: TRUE Depends: R (>= 4.1.0), - photobiology (>= 0.11.2), + photobiology (>= 0.11.4.9003), ggplot2 (>= 3.5.0) Imports: photobiologyWavebands (>= 0.5.2), diff --git a/NEWS.md b/NEWS.md index 5ddfa833..8748850f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,14 @@ editor_options: wrap: 72 --- +# ggspectra 0.4.0 + +- Update for compatibility with 'photobiology' (>= 0.12.0), which is required. +- `autoplot()` methods no longer support normalization on-the-fly, but existing +normalization is updated when the unit or quantity is modified. +- The argument passed to `idfactor` when plotting multiple spectra stored in +long form, can be used to rename the existing idfactor of the spectral object. + # ggspectra 0.3.15 - Fix a bug in `autotitle()` affecting only collections of spectra where all diff --git a/R/autoplot-calibration-spct.R b/R/autoplot-calibration-spct.R index 93c0f7c9..964e1862 100644 --- a/R/autoplot-calibration-spct.R +++ b/R/autoplot-calibration-spct.R @@ -270,7 +270,7 @@ autoplot.calibration_spct <- geom = "line", time.format = "", tz = "UTC", - norm = NULL, + norm = NA, text.size = 2.5, idfactor = NULL, facets = FALSE, @@ -279,12 +279,9 @@ autoplot.calibration_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor) if (plot.data != "as.is") { return( @@ -312,8 +309,6 @@ autoplot.calibration_spct <- ) } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "colour.guide", "peaks")) @@ -361,8 +356,7 @@ autoplot.calibration_mspct <- ..., range = getOption("ggspectra.wlrange", default = NULL), unit.out = "ignored", - norm = getOption("ggspectra.normalize", - default = "skip"), + norm = NA, pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", idfactor = TRUE, @@ -371,8 +365,9 @@ autoplot.calibration_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- trim_wl(object, range = range, use.hinges = TRUE, fill = NULL) @@ -395,7 +390,7 @@ autoplot.calibration_mspct <- unit.out = unit.out, norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -408,7 +403,7 @@ autoplot.calibration_mspct <- unit.out = unit.out, norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, diff --git a/R/autoplot-cps-spct.r b/R/autoplot-cps-spct.r index 750ae1f0..d5dbc618 100644 --- a/R/autoplot-cps-spct.r +++ b/R/autoplot-cps-spct.r @@ -253,7 +253,7 @@ autoplot.cps_spct <- w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, unit.out = NULL, pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = "mean", @@ -271,12 +271,10 @@ autoplot.cps_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) if (plot.data != "as.is") { return( @@ -304,22 +302,12 @@ autoplot.cps_spct <- ) } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "colour.guide", "peaks")) annotations <- decode_annotations(annotations, annotations.default) - # avoid warning in 'photobiology' (== 0.10.10) - if (is.character(norm) && norm == "update" && !is_normalized(object)) { - norm <- "skip" - } - # normalization skipping is handled by normalize() - object <- photobiology::normalize(x = object, - range = range, - norm = norm, - na.rm = na.rm) + if (length(w.band) == 0) { if (is.null(range)) { w.band <- waveband(object) @@ -370,8 +358,9 @@ autoplot.cps_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- photobiology::trim_wl(object, @@ -379,15 +368,6 @@ autoplot.cps_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, - na.rm = na.rm) - norm <- "skip" - } # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -405,7 +385,7 @@ autoplot.cps_mspct <- range = getOption("ggspectra.wlrange", default = NULL), norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -417,7 +397,7 @@ autoplot.cps_mspct <- range = getOption("ggspectra.wlrange", default = NULL), norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, diff --git a/R/autoplot-filter-spct.r b/R/autoplot-filter-spct.r index ed0fb0fc..7d207faa 100644 --- a/R/autoplot-filter-spct.r +++ b/R/autoplot-filter-spct.r @@ -57,7 +57,7 @@ Afr_plot <- function(spct, ylim, na.rm, ...) { - if (!is.filter_spct(spct)) { + if (!photobiology::is.filter_spct(spct)) { stop("Afr_plot() can only plot filter_spct objects.") } @@ -65,15 +65,16 @@ Afr_plot <- function(spct, ylim <- rep(NA_real_, 2L) } force(spct) - spct <- any2Afr(spct, action = "add") + spct <- photobiology::any2Afr(spct, action = "add") if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- + photobiology::trim_wl(w.band, range = photobiology::wl_range(spct)) } - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent not supported for scaled spectral data.") pc.out <- FALSE @@ -82,9 +83,9 @@ Afr_plot <- function(spct, s.Afr.label <- expression(Spectral~~absorptance~~italic(A)[lambda]~~("rel.")) Afr.label.total <- "atop(italic(A), (rel))" Afr.label.avg <- "atop(bar(italic(A)[lambda]), (rel))" - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { warning("Plotting of normalized absorptance not supported") - return(ggplot()) + return(ggplot2::ggplot()) } else if (pc.out) { scale.factor <- 100 s.Afr.label <- expression(Spectral~~absorptance~~italic(A)[lambda]~~("%")) @@ -136,7 +137,9 @@ Afr_plot <- function(spct, y.max <- max(spct[["Afr"]], 1, y.min, na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["Afr"]])) + plot <- + ggplot2::ggplot(spct, + ggplot2::aes(x = .data[["w.length"]], y = .data[["Afr"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -147,37 +150,48 @@ Afr_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.max > 1.005) { - plot <- plot + geom_hline(yintercept = 1, linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 1, linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "black") } if (y.min < -0.005) { - plot <- plot + geom_hline(yintercept = 0, - linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, - linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "black") } } if (!is.null(geom) && geom %in% c("area", "spct")) { - plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) + plot <- + plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.Afr.label) + plot <- + plot + ggplot2::geom_line(na.rm = na.rm) + plot <- + plot + ggplot2::labs(x = expression("Wavelength, "*lambda~(nm)), + y = s.Afr.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, label.mult = scale.factor, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -188,23 +202,29 @@ Afr_plot <- function(spct, na.rm = TRUE) if (!is.null(annotations) && - length(intersect(c("labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { + length(intersect(c("labels", "summaries", "colour.guide", "reserve.space"), + annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- c(photobiology::wl_min(spct) - + photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max) - x.limits <- range(spct) + x.limits <- photobiology::wl_range(spct) } if (pc.out) { - plot <- plot + scale_y_continuous(labels = scales::percent, breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(labels = scales::percent, + breaks = y.breaks, + limits = y.limits) } else { - plot <- plot + scale_y_continuous(breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(breaks = y.breaks, + limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } @@ -270,7 +290,7 @@ T_plot <- function(spct, na.rm, ylim, ...) { - if (!is.filter_spct(spct)) { + if (!photobiology::is.filter_spct(spct)) { stop("T_plot() can only plot filter_spct objects.") } if (!is.null(geom) && !geom %in% c("area", "line", "spct")) { @@ -281,29 +301,29 @@ T_plot <- function(spct, ylim <- rep(NA_real_, 2L) } force(spct) - spct <- any2T(spct, action = "replace") + spct <- photobiology::any2T(spct, action = "replace") if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } - Tfr.type <- getTfrType(spct) + Tfr.type <- photobiology::getTfrType(spct) if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- trim_wl(w.band, range = photobiology::wl_range(spct)) } if (!length(Tfr.type)) { Tfr.type <- "unknown" } Tfr.tag <- switch(Tfr.type, - internal = "int", - total = "tot", + internal = "int", + total = "tot", unknown = "", - NA_character_) - Tfr.name <- switch(Tfr.type, - internal = "Internal", - total = "Total", - unknown = "Unknown-type", NA_character_) + Tfr.name <- switch(Tfr.type, + internal = "Internal", + total = "Total", + unknown = "Unknown-type", + NA_character_) - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent not supported for scaled spectral data.") pc.out <- FALSE @@ -312,13 +332,13 @@ T_plot <- function(spct, s.Tfr.label <- bquote(.(Tfr.name)~~spectral~~transmittance~~k %*% T[lambda]^{.(Tfr.tag)}~~("rel.")) Tfr.label.total <- paste("k %*% T^{", Tfr.tag,"}", sep = "") Tfr.label.avg <- paste("bar(k %*% T[lambda]^{", Tfr.tag, "})", sep = "") - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { if (pc.out) { warning("Percent not supported for normalized spectral data.") pc.out <- FALSE } scale.factor <- 1 - norm <- round(getNormalization(spct)[["norm.wl"]], 1) + norm <- round(photobiology::getNormalization(spct)[["norm.wl"]], 1) s.Tfr.label <- bquote(.(Tfr.name)~~spectral~~transmittance~~T[lambda]^{.(Tfr.tag)}/T[lambda==.(norm)]^{.(Tfr.tag)}~~("rel.")) Tfr.label.total <- paste("atop(T^{", Tfr.tag, "}, T[lambda == ", norm, "]^{", Tfr.tag, "}", @@ -377,7 +397,9 @@ T_plot <- function(spct, y.max <- max(c(spct[["Tfr"]], 1), na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["Tfr"]])) + plot <- + ggplot2::ggplot(spct, + ggplot2::aes(x = .data[["w.length"]], y = .data[["Tfr"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -388,39 +410,44 @@ T_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.max > 1.005) { - plot <- plot + geom_hline(yintercept = 1, - linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 1, - linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "black") } if (y.min < -0.005) { - plot <- plot + geom_hline(yintercept = 0, - linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, - linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "black") } } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.Tfr.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, label.mult = scale.factor, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -439,14 +466,18 @@ T_plot <- function(spct, x.limits <- range(spct) } if (pc.out) { - plot <- plot + scale_y_continuous(labels = scales::percent, breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(labels = scales::percent, breaks = y.breaks, + limits = y.limits) } else { - plot <- plot + scale_y_continuous(breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(breaks = y.breaks, + limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } @@ -510,7 +541,7 @@ A_plot <- function(spct, na.rm, ylim, ...) { - if (!is.filter_spct(spct)) { + if (!photobiology::is.filter_spct(spct)) { stop("A_plot() can only plot filter_spct objects.") } if (!is.null(geom) && !geom %in% c("area", "line", "spct")) { @@ -520,14 +551,14 @@ A_plot <- function(spct, if (is.null(ylim) || !is.numeric(ylim)) { ylim <- rep(NA_real_, 2L) } - spct <- any2A(spct, action = "replace") + spct <- photobiology::any2A(spct, action = "replace") if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, range = photobiology::wl_range(spct)) } - Tfr.type <- getTfrType(spct) + Tfr.type <- photobiology::getTfrType(spct) if (!length(Tfr.type)) { Tfr.type <- "unknown" } @@ -541,11 +572,11 @@ A_plot <- function(spct, total = "Total", unknown = "Unknown-type", NA_character_) - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { s.A.label <- bquote(.(Tfr.name)~~spectral~~absorbance~~k %*% A[lambda]^{.(Tfr.tag)}~~("rel.")) A.label.total <- paste("k %*% A^{", Tfr.tag, "}", sep = "") A.label.avg <- paste("bar(k %*% A[lambda]^{", Tfr.tag, "})", sep = "") - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { norm <- round(getNormalization(spct)[["norm.wl"]], 1) s.A.label <- bquote(.(Tfr.name)~~spectral~~absorbance~~A[lambda]^{.(Tfr.tag)}/A[lambda==.(norm)]^{.(Tfr.tag)}~~("rel.")) A.label.total <- paste("atop(A^{", Tfr.tag, @@ -581,8 +612,8 @@ A_plot <- function(spct, if (!is.na(ylim[1])) { y.min <- ylim[1] spct[["A"]] <- ifelse(spct[["A"]] < y.min, - NA_real_, - spct[["A"]]) + NA_real_, + spct[["A"]]) } else { y.min <- min(c(spct[["A"]], 0), na.rm = TRUE) } @@ -590,13 +621,15 @@ A_plot <- function(spct, if (!is.na(ylim[2])) { y.max <- ylim[2] spct[["A"]] <- ifelse(spct[["A"]] > y.max, - NA_real_, - spct[["A"]]) + NA_real_, + spct[["A"]]) } else { y.max <- max(spct[["A"]], na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["A"]])) + plot <- + ggplot2::ggplot(spct, + ggplot2::aes(x = .data[["w.length"]], y = .data[["A"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -607,12 +640,18 @@ A_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.max > 6) { - plot <- plot + geom_hline(yintercept = 6, linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 6, + linetype = "dashed", colour = "red") } if (y.min < -0.01) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "black") } } @@ -626,13 +665,14 @@ A_plot <- function(spct, return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, y.max = min(y.max, 6), y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -643,15 +683,17 @@ A_plot <- function(spct, na.rm = TRUE) if (!is.null(annotations) && - length(intersect(c("boxes", "segments", "labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { + length(intersect(c("boxes", "segments", "labels", "summaries", + "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, min(y.max, 6) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- c(min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, min(y.max, 6)) x.limits <- range(spct) } - plot <- plot + scale_y_continuous(limits = y.limits) - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot <- plot + ggplot2::scale_y_continuous(limits = y.limits) + plot + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } @@ -754,13 +796,13 @@ R_plot <- function(spct, unknown = "Unknown-type", NA_character_) - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { scale.factor <- 1 s.Rfr.label <- bquote(.(Rfr.name)~~spectral~~reflectance~~k %*% R[lambda]^{.(Rfr.tag)}~~("rel.")) Rfr.label.total <- paste("k %*% R^{", Rfr.tag, "}", sep = "") Rfr.label.avg <- paste("bar(k %*% R[lambda]^{", Rfr.tag, "})", sep = "") - } else if (is_normalized(spct)) { - norm <- round(getNormalization(spct)[["norm.wl"]], 1) + } else if (photobiology::is_normalized(spct)) { + norm <- round(photobiology::getNormalization(spct)[["norm.wl"]], 1) s.Rfr.label <- bquote(.(Rfr.name)~~spectral~~reflectance~~R[lambda]^{.(Rfr.tag)}/R[lambda==.(norm)]^{.(Rfr.tag)}~~("rel.")) Rfr.label.total <- paste("atop(R^{", Rfr.tag, "}, R[lambda == ", norm, "]^{", Rfr.tag, "})", @@ -819,7 +861,7 @@ R_plot <- function(spct, y.max <- max(c(spct[["Rfr"]], 1), na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["Rfr"]])) + plot <- ggplot2::ggplot(spct, aes(x = .data[["w.length"]], y = .data[["Rfr"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -830,34 +872,44 @@ R_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.max > 1.005) { - plot <- plot + geom_hline(yintercept = 1, linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 1, linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 1, + linetype = "dashed", colour = "black") } if (y.min < -0.005) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "red") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- + plot + ggplot2::geom_hline(yintercept = 0, + linetype = "dashed", colour = "black") } } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.Rfr.label) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) + plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), + y = s.Rfr.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -870,20 +922,24 @@ R_plot <- function(spct, if (!is.null(annotations) && length(intersect(c("labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- c(min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max) - x.limits <- range(spct) + x.limits <- photobiology::wl_range(spct) } if (pc.out) { - plot <- plot + scale_y_continuous(labels = scales::percent, breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(labels = scales::percent, + breaks = y.breaks, + limits = y.limits) } else { - plot <- plot + scale_y_continuous(breaks = y.breaks, - limits = y.limits) + plot <- + plot + ggplot2::scale_y_continuous(breaks = y.breaks, + limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } #' Create a complete ggplot for a object spectrum. @@ -937,10 +993,10 @@ O_plot <- function(spct, facets, na.rm, ylim) { - if (!is.object_spct(spct)) { + if (!photobiology::is.object_spct(spct)) { stop("O_plot() can only plot object_spct objects.") } - if (getMultipleWl(spct) > 1L && (is.null(facets) || !facets)) { + if (photobiology::getMultipleWl(spct) > 1L && (is.null(facets) || !facets)) { warning("Only one object spectrum per panel supported") facets <- TRUE } else if (is.null(facets)) { @@ -961,10 +1017,11 @@ O_plot <- function(spct, warning("'ylim' not supported for stacked plots!") } if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, + range = photobiology::wl_range(spct)) } Rfr.type <- getRfrType(spct) if (length(Rfr.type) == 0) { @@ -979,7 +1036,7 @@ O_plot <- function(spct, } if (Tfr.type == "internal") { # warning("Internal transmittance converted to total transmittance") - spct <- convertTfrType(spct, Tfr.type = "total") + spct <- photobiology::convertTfrType(spct, Tfr.type = "total") } s.Rfr.label <- expression(atop(Spectral~~reflectance~R[lambda]~~absorptance~~A[lambda], and~~transmittance~T[lambda])) spct[["Afr"]] <- 1.0 - spct[["Tfr"]] - spct[["Rfr"]] @@ -1033,55 +1090,73 @@ O_plot <- function(spct, } } - idfactor <- getIdFactor(spct) # needed as we will get a tibble back - molten.tb <- photobiology::spct_wide2long(spct, idfactor = "variable", rm.spct.class = TRUE) + idfactor <- + photobiology::getIdFactor(spct) # needed as we will get a tibble back + molten.tb <- + photobiology::spct_wide2long(spct, idfactor = "variable", rm.spct.class = TRUE) - plot <- ggplot(molten.tb, aes(x = .data[["w.length"]], y = .data[["value"]])) - attributes(plot[["data"]]) <- c(attributes(plot[["data"]]), get_attributes(spct)) + plot <- + ggplot2::ggplot(molten.tb, aes(x = .data[["w.length"]], y = .data[["value"]])) + attributes(plot[["data"]]) <- c(attributes(plot[["data"]]), + photobiology::get_attributes(spct)) if (stacked) { if (is.null(geom) || geom %in% c("spct", "area")) { - plot <- plot + geom_area(aes(alpha = .data[["variable"]]), fill = "black", colour = NA) - plot <- plot + scale_alpha_manual(values = c(Tfr = 0.4, - Rfr = 0.25, - Afr = 0.55), - breaks = c("Rfr", "Afr", "Tfr"), - labels = c(Tfr = expression(T[lambda]), - Afr = expression(A[lambda]), - Rfr = expression(R[lambda])), - guide = guide_legend(title = NULL)) - } else { - plot <- plot + geom_line(aes(linetype = .data[["variable"]]), - position = position_stack()) - plot <- plot + scale_linetype(labels = c(Tfr = expression(T[lambda]), + plot <- + plot + geom_area(aes(alpha = .data[["variable"]]), + fill = "black", colour = NA) + plot <- + plot + + ggplot2::scale_alpha_manual(values = c(Tfr = 0.4, + Rfr = 0.25, + Afr = 0.55), + breaks = c("Rfr", "Afr", "Tfr"), + labels = c(Tfr = expression(T[lambda]), Afr = expression(A[lambda]), Rfr = expression(R[lambda])), guide = guide_legend(title = NULL)) + } else { + plot <- + plot + ggplot2::geom_line(aes(linetype = .data[["variable"]]), + position = ggplot2::position_stack()) + plot <- + plot + + ggplot2::scale_linetype(labels = c(Tfr = expression(T[lambda]), + Afr = expression(A[lambda]), + Rfr = expression(R[lambda])), + guide = guide_legend(title = NULL)) } } else { if (!is.null(geom) && geom %in% c("spct", "area")) { plot <- plot + geom_spct(aes(group = .data[["variable"]]), fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(aes(linetype = .data[["variable"]])) - plot <- plot + scale_linetype(labels = c(Tfr = expression(T[lambda]), - Afr = expression(A[lambda]), - Rfr = expression(R[lambda])), - guide = guide_legend(title = NULL)) + plot <- + plot + + ggplot2::geom_line(aes(linetype = .data[["variable"]])) + plot <- + plot + + ggplot2::scale_linetype(labels = c(Tfr = expression(T[lambda]), + Afr = expression(A[lambda]), + Rfr = expression(R[lambda])), + guide = ggplot2::guide_legend(title = NULL)) } if (is.numeric(facets)) { plot <- plot + - facet_wrap(facets = vars(.data[[idfactor]]), ncol = as.integer(facets)) + ggplot2::facet_wrap(facets = vars(.data[[idfactor]]), + ncol = as.integer(facets)) } else if (facets) { plot <- plot + - facet_wrap(facets = vars(.data[[idfactor]])) + ggplot2::facet_wrap(facets = vars(.data[[idfactor]])) } - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.Rfr.label) + plot <- + plot + ggplot2::labs(x = expression("Wavelength, "*lambda~(nm)), y = s.Rfr.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() valid.annotations <- c("labels", "boxes", "segments", "colour.guide", "reserve.space") if (!stacked) { @@ -1092,8 +1167,8 @@ O_plot <- function(spct, plot <- plot + decoration(w.band = w.band, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -1105,10 +1180,11 @@ O_plot <- function(spct, if (!is.null(annotations) && length(intersect(c("boxes", "segments", "labels", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) + x.limits <- + c(photobiology::wl_min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) } else { y.limits <- c(y.min, y.max) - x.limits <- range(spct) + x.limits <- photobiology::wl_range(spct) } if (pc.out) { plot <- plot + @@ -1117,12 +1193,12 @@ O_plot <- function(spct, limits = y.limits) } else { plot <- - plot + scale_y_continuous(breaks = y.breaks, - limits = y.limits) + plot + ggplot2::scale_y_continuous(breaks = y.breaks, + limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, - breaks = scales::pretty_breaks(n = 7)) + plot + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } @@ -1168,13 +1244,13 @@ O_plot <- function(spct, #' autoplot(yellow_gel.spct) #' autoplot(yellow_gel.spct, geom = "spct") #' autoplot(yellow_gel.spct, plot.qty = "transmittance") -#' autoplot(yellow_gel.spct, plot.qty = "absorptance") #' autoplot(yellow_gel.spct, plot.qty = "absorbance") #' autoplot(yellow_gel.spct, pc.out = TRUE) #' autoplot(yellow_gel.spct, annotations = c("+", "wls")) #' #' # spectra for two filters in long form #' autoplot(two_filters.spct) +#' autoplot(two_filters.spct, idfactor = TRUE) #' autoplot(two_filters.spct, idfactor = "Spectra") #' autoplot(two_filters.spct, facets = TRUE) #' @@ -1190,8 +1266,7 @@ autoplot.filter_spct <- w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "update"), + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "transmittance"), pc.out = getOption("ggspectra.pc.out", @@ -1212,19 +1287,16 @@ autoplot.filter_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) if (plot.data != "as.is") { return( - autoplot(object = subset2mspct(object), + autoplot(object = photobiology::subset2mspct(object), w.band = w.band, range = range, - norm = norm, plot.qty = plot.qty, pc.out = pc.out, label.qty = label.qty, @@ -1245,19 +1317,11 @@ autoplot.filter_spct <- ) } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "summaries", "colour.guide", "peaks")) annotations <- decode_annotations(annotations, annotations.default) - # normalization updated and quantity changed in one go - object <- photobiology::normalize(x = object, - range = range, - norm = norm, - qty.out = plot.qty, - na.rm = na.rm) if (is.null(label.qty)) { if (photobiology::is_normalized(object) || photobiology::is_scaled(object)) { @@ -1328,10 +1392,10 @@ autoplot.filter_spct <- } out.ggplot + autotitle(object = object, - time.format = time.format, - tz = tz, - object.label = object.label, - annotations = annotations) + time.format = time.format, + tz = tz, + object.label = object.label, + annotations = annotations) } #' @rdname autoplot.filter_spct @@ -1342,8 +1406,7 @@ autoplot.filter_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "update"), + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "transmittance"), pc.out = getOption("ggspectra.pc.out", @@ -1355,27 +1418,20 @@ autoplot.filter_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) - # We trim the spectra to avoid unnecesary computaions later + # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- photobiology::trim_wl(object, range = range, use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - norm = norm, - qty.out = plot.qty, - na.rm = na.rm) - norm <- "skip" - } # we convert spectra to the quantity to be plotted object <- switch(plot.qty, transmittance = any2T(object, action = "replace"), absorbance = any2A(object, action = "replace"), # we need to discard T´Rfr if present - absorptance = msmsply(any2Afr(object, action = "replace"), `[`, i = TRUE, j = c("w.length", "Afr"))) + absorptance = msmsply(any2Afr(object, action = "replace"), + `[`, i = TRUE, j = c("w.length", "Afr"))) # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -1390,13 +1446,12 @@ autoplot.filter_mspct <- se = photobiology::s_se(object) ) col.name <- c(transmittance = "Tfr", absorptance = "Afr", absorbance = "A") - if (is.filter_spct(z) && col.name[plot.qty] %in% names(z)) { + if (photobiology::is.filter_spct(z) && col.name[plot.qty] %in% names(z)) { autoplot(object = z, range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, plot.qty = plot.qty, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -1407,9 +1462,8 @@ autoplot.filter_mspct <- autoplot(object = z, y.name = paste(col.name[plot.qty], plot.data, sep = "."), range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -1457,8 +1511,7 @@ autoplot.reflector_spct <- w.band=getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "update"), + norm = NA, plot.qty = getOption("photobiology.reflector.qty", default = "reflectance"), pc.out = getOption("ggspectra.pc.out", @@ -1479,19 +1532,16 @@ autoplot.reflector_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) if (plot.data != "as.is") { return( - autoplot(object = subset2mspct(object), + autoplot(object = photobiology::subset2mspct(object), w.band = w.band, range = range, - norm = norm, plot.qty = plot.qty, pc.out = pc.out, label.qty = label.qty, @@ -1512,19 +1562,12 @@ autoplot.reflector_spct <- ) } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "summaries", "colour.guide", "peaks")) annotations <- decode_annotations(annotations, annotations.default) - # normalization needs to be redone if unit.out has changed - object <- photobiology::normalize(x = object, - range = range, - norm = norm, - qty.out = plot.qty, - na.rm = na.rm) + if (is.null(label.qty)) { if (photobiology::is_normalized(object) || photobiology::is_scaled(object)) { @@ -1578,7 +1621,7 @@ autoplot.reflector_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.normalize", default = "update"), + norm = NA, plot.qty = getOption("photobiology.reflector.qty", default = "reflectance"), pc.out = getOption("ggspectra.pc.out", @@ -1590,8 +1633,9 @@ autoplot.reflector_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- photobiology::trim_wl(object, @@ -1599,15 +1643,7 @@ autoplot.reflector_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - norm = norm, - qty.out = plot.qty, - na.rm = na.rm) - norm <- "skip" - } + # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -1620,13 +1656,12 @@ autoplot.reflector_mspct <- sd = photobiology::s_sd(object), se = photobiology::s_se(object) ) - if (is.reflector_spct(z) && "Rfr" %in% names(z)) { + if (photobiology::is.reflector_spct(z) && "Rfr" %in% names(z)) { autoplot(object = z, range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, plot.qty = plot.qty, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -1636,9 +1671,8 @@ autoplot.reflector_mspct <- autoplot(object = z, y.name = paste("Rfr", plot.data, sep = "."), range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -1708,7 +1742,7 @@ autoplot.object_spct <- w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, plot.qty = "all", pc.out = getOption("ggspectra.pc.out", default = FALSE), @@ -1729,19 +1763,16 @@ autoplot.object_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) if (plot.data != "as.is") { return( - autoplot(object = subset2mspct(object), + autoplot(object = photobiology::subset2mspct(object, idfactor = idfactor), w.band = w.band, range = range, - norm = norm, plot.qty = plot.qty, pc.out = pc.out, label.qty = label.qty, @@ -1763,12 +1794,11 @@ autoplot.object_spct <- ) } - force(object.label) if (is.null(plot.qty)) { plot.qty <- "all" } if (is.null(facets)) { - facets <- plot.qty == "all" && getMultipleWl(object) > 1L + facets <- plot.qty == "all" && photobiology::getMultipleWl(object) > 1L } if (plot.qty == "all") { @@ -1829,7 +1859,6 @@ autoplot.object_spct <- autoplot(object = object, w.band = w.band, range = range, - norm = norm, plot.qty = plot.qty, pc.out = pc.out, label.qty = label.qty, @@ -1857,7 +1886,7 @@ autoplot.object_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "all"), pc.out = getOption("ggspectra.pc.out", @@ -1869,8 +1898,9 @@ autoplot.object_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # facets will be forced later for "all" with a warning if (plot.qty == "reflectance") { object <- photobiology::as.reflector_mspct(object) @@ -1884,15 +1914,7 @@ autoplot.object_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is" && plot.qty != "all") { - object <- photobiology::normalize(object, - norm = norm, - qty.out = plot.qty, - na.rm = na.rm) - norm <- "skip" - } + # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -1906,39 +1928,36 @@ autoplot.object_mspct <- se = photobiology::s_se(object) ) col.name <- c(transmittance = "Tfr", absorptance = "Afr", reflectance = "Rfr") - if ((is.object_spct(z) && sum(col.name %in% names(z)) >= 2) || - (is.filter_spct(z) && any(c("Tfr", "Afr", "A")) %in% names(z)) || - (is.reflector_spct(z) && "Rfr" %in% names(z))) { + if ((photobiology::is.object_spct(z) && sum(col.name %in% names(z)) >= 2) || + (photobiology::is.filter_spct(z) && any(c("Tfr", "Afr", "A")) %in% names(z)) || + (photobiology::is.reflector_spct(z) && "Rfr" %in% names(z))) { autoplot(object = z, range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, plot.qty = plot.qty, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, ...) - } else if (is.filter_spct(z) && !any(col.name %in% names(z))) { - z <- as.generic_spct(z) + } else if (photobiology::is.filter_spct(z) && !any(col.name %in% names(z))) { + z <- photobiology::as.generic_spct(z) autoplot(object = z, y.name = paste(col.name[plot.qty], plot.data, sep = "."), range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, ...) - } else if (is.reflector_spct(z) && !"Rfr" %in% names(z)) { - z <- as.generic_spct(z) + } else if (photobiology::is.reflector_spct(z) && !"Rfr" %in% names(z)) { + z <- photobiology::as.generic_spct(z) autoplot(object = z, y.name = paste("Rfr", plot.data, sep = "."), range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, diff --git a/R/autoplot-generic-spct.R b/R/autoplot-generic-spct.R index 94f27094..aa73d39b 100644 --- a/R/autoplot-generic-spct.R +++ b/R/autoplot-generic-spct.R @@ -203,6 +203,7 @@ generic_plot <- function(spct, #' #' sun.generic_spct <- as.generic_spct(sun.spct) #' autoplot(sun.generic_spct, y.name = "s.q.irrad") +#' autoplot(sun.generic_spct, y.name = "s.e.irrad") #' autoplot(sun.generic_spct, y.name = "s.q.irrad", #' annotations = "") #' autoplot(sun.generic_spct, y.name = "s.q.irrad", @@ -227,6 +228,7 @@ autoplot.generic_spct <- w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), + norm = NA, label.qty = "none", span = NULL, wls.target = "HM", @@ -241,6 +243,8 @@ autoplot.generic_spct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + check_idfactor_arg(object, idfactor = idfactor) annotations.default <- getOption("photobiology.plot.annotations", @@ -285,6 +289,6 @@ autoplot.generic_spct <- #' @export #' autoplot.generic_mspct <- function(object, ...) { - warning("No specialized 'autoplot()' method exist for objects of class generic_mspct.") + warning("No specialized 'autoplot()' method exists for objects of class generic_mspct.") ggplot() } diff --git a/R/autoplot-raw-spct.r b/R/autoplot-raw-spct.r index 0ab5a5fd..1e20bf08 100644 --- a/R/autoplot-raw-spct.r +++ b/R/autoplot-raw-spct.r @@ -54,14 +54,13 @@ raw_plot <- function(spct, wls.target, annotations, geom, - relative, text.size, idfactor, facets, ylim, na.rm) { if (!is.raw_spct(spct)) { - stop("raw_plot() can only plot response_spct objects.") + stop("raw_plot() can only plot 'raw_spct' objects.") } if (!is.null(geom) && !geom %in% c("area", "line", "spct")) { warning("'geom = ", geom, "' not supported, using default instead.") @@ -281,10 +280,12 @@ raw_plot <- function(spct, #' @family autoplot methods #' autoplot.raw_spct <- - function(object, ..., + function(object, + ..., w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), + norm = NA, unit.out = "counts", pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = "mean", @@ -294,7 +295,6 @@ autoplot.raw_spct <- geom = "line", time.format = "", tz = "UTC", - norm = "skip", text.size = 2.5, idfactor = NULL, facets = FALSE, @@ -303,19 +303,16 @@ autoplot.raw_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) - if (plot.data != "as.is") { + if (photobiology::getMultipleWl(object) > 1L && plot.data != "as.is") { return( autoplot(object = subset2mspct(object), w.band = w.band, range = range, - norm = norm, unit.out = unit.out, pc.out = pc.out, label.qty = label.qty, @@ -336,23 +333,13 @@ autoplot.raw_spct <- ) } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "colour.guide", "peaks", "boundaries")) annotations <- decode_annotations(annotations, annotations.default) - # avoid warning in 'photobiology' (== 0.10.10) - if (is.character(norm) && norm == "update" && !is_normalized(object)) { - norm <- "skip" - } - # normalization skipping is handled by normalize() - object <- photobiology::normalize(x = object, - range = range, - norm = norm, - na.rm = na.rm) + if (length(w.band) == 0) { if (is.null(range)) { w.band <- waveband(object) @@ -392,8 +379,7 @@ autoplot.raw_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "skip"), + norm = NA, unit.out = "counts", pc.out = getOption("ggspectra.pc.out", default = FALSE), idfactor = TRUE, @@ -403,8 +389,9 @@ autoplot.raw_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecesary computaions later if (!is.null(range)) { object <- photobiology::trim_wl(object, @@ -412,15 +399,6 @@ autoplot.raw_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, - na.rm = na.rm) - norm <- "skip" - } # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -439,7 +417,7 @@ autoplot.raw_mspct <- norm = norm, unit.out = unit.out, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -451,7 +429,7 @@ autoplot.raw_mspct <- range = getOption("ggspectra.wlrange", default = NULL), norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, diff --git a/R/autoplot-response-spct.r b/R/autoplot-response-spct.r index b588b162..7d3e6172 100644 --- a/R/autoplot-response-spct.r +++ b/R/autoplot-response-spct.r @@ -56,7 +56,7 @@ e_rsp_plot <- function(spct, facets, ylim, na.rm) { - if (!is.response_spct(spct)) { + if (!photobiology::is.response_spct(spct)) { stop("e_Rsp_plot() can only plot response_spct objects.") } spct[["s.q.response"]] <- NULL @@ -68,15 +68,15 @@ e_rsp_plot <- function(spct, ylim <- rep(NA_real_, 2L) } if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, range = photobiology::wl_range(spct)) } exposure.label <- NA - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent scale supported only for normalized cps_spct objects.") pc.out <- FALSE @@ -84,7 +84,7 @@ e_rsp_plot <- function(spct, s.rsp.label <- expression(Spectral~~energy~~response~~k %*% R[E~lambda]~~("rel.")) rsp.label.total <- "atop(k %*% R[E], (\"rel.\"))" rsp.label.avg <- "atop(bar(k %*% R[E~lambda]), (\"rel.\"))" - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { if (!pc.out) { multiplier.label <- "rel." } else { @@ -101,31 +101,31 @@ e_rsp_plot <- function(spct, warning("Percent scale supported only for normalized cps_spct objects.") pc.out <- FALSE } - time.unit <- getTimeUnit(spct) + time.unit <- photobiology::getTimeUnit(spct) if (!length(time.unit)) { time.unit <- "unkonwn" } time.unit.char <- duration2character(time.unit) - if (time.unit.char=="second") { + if (time.unit.char == "second") { s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~s^{-1}~nm^{-1})) rsp.label.total <- "atop(R[E], (resp.~~unit~~s^{-1}))" rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~s^{-1}~nm^{-1}))" - } else if (time.unit.char=="day") { + } else if (time.unit.char == "day") { s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~d^{-1}~nm^{-1})) rsp.label.total <- "atop(R[E], (resp.~~unit~~d^{-1}))" rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~d^{-1}~nm^{-1}))" - } else if (time.unit.char=="hour") { + } else if (time.unit.char == "hour") { s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~~h^{-1}~nm^{-1})) rsp.label.total <- "atop(R[E], (resp.~~unit~~h^{-1}))" rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~~h^{-1}~nm^{-1}))" - } else if (time.unit.char=="duration") { + } else if (time.unit.char == "duration") { s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~nm^{-1})) rsp.label.total <- "atop(R[E], (resp.~~unit))" rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~nm^{-1}))" exposure.label <- paste("Length of time:", ifelse(lubridate::is.duration(time.unit), as.character(time.unit), "unknown")) - } else if (time.unit.char=="exposure") { + } else if (time.unit.char == "exposure") { s.rsp.label <- expression(Spectral~~energy~~response~~R[E~lambda]~~(resp.~~unit~nm^{-1})) rsp.label.total <- "atop(R[E], (resp.~~unit))" rsp.label.avg <- "atop(bar(R[E~lambda]), (resp.~~unit~nm^{-1}))" @@ -139,8 +139,8 @@ e_rsp_plot <- function(spct, if (!is.na(ylim[1])) { y.min <- ylim[1] spct[["s.e.response"]] <- ifelse(spct[["s.e.response"]] < y.min, - NA_real_, - spct[["s.e.response"]]) + NA_real_, + spct[["s.e.response"]]) } else { y.min <- min(spct[["s.e.response"]], 0, na.rm = TRUE) } @@ -148,8 +148,8 @@ e_rsp_plot <- function(spct, if (!is.na(ylim[2])) { y.max <- ylim[2] spct[["s.e.response"]] <- ifelse(spct[["s.e.response"]] > y.max, - NA_real_, - spct[["s.e.response"]]) + NA_real_, + spct[["s.e.response"]]) } else { y.max <- max(spct[["s.e.response"]], y.min, 0, na.rm = TRUE) } @@ -170,7 +170,8 @@ e_rsp_plot <- function(spct, rsp.label <- "" } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.e.response"]])) + plot <- ggplot2::ggplot(spct, aes(x = .data[["w.length"]], + y = .data[["s.e.response"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -181,26 +182,28 @@ e_rsp_plot <- function(spct, # We want data plotted on top of the boundary lines # Negative response is valid! if ("boundaries" %in% annotations) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "black") } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.rsp.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- plot + + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -210,33 +213,37 @@ e_rsp_plot <- function(spct, na.rm = TRUE) if (!is.na(exposure.label)) { - plot <- plot + annotate("text", - x = min(spct), - y = y.max, - label = exposure.label, - vjust = -0.5, - hjust = 0, - size = rel(3), - na.rm = TRUE ) + plot <- plot + ggplot2::annotate("text", + x = photobiology::wl_min(spct), + y = y.max, + label = exposure.label, + vjust = -0.5, + hjust = 0, + size = rel(3), + na.rm = TRUE ) } if (!is.null(annotations) && length(intersect(c("boxes", "segments", "labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- + c(min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max) - x.limits <- range(spct) + x.limits <- photobiology::wl_range(spct) } if (abs(y.min) < 5e-2 && (abs(y.max - 1) < 5.e-2)) { plot <- plot + - scale_y_continuous(breaks = c(0, 0.25, 0.5, 0.75, 1), limits = y.limits) + ggplot2::scale_y_continuous(breaks = c(0, 0.25, 0.5, 0.75, 1), + limits = y.limits) } else { - plot <- plot + scale_y_continuous(limits = y.limits) + plot <- plot + ggplot2::scale_y_continuous(limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } #' Create a complete ggplot for response spectra. @@ -297,7 +304,7 @@ q_rsp_plot <- function(spct, facets, ylim, na.rm) { - if (!is.response_spct(spct)) { + if (!photobiology::is.response_spct(spct)) { stop("q_Rsp_plot() can only plot response_spct objects.") } spct[["s.e.response"]] <- NULL @@ -309,15 +316,16 @@ q_rsp_plot <- function(spct, ylim <- rep(NA_real_, 2L) } if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, + range = photobiology::wl_range(spct)) } exposure.label <- NA - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent scale supported only for normalized response_spct objects.") pc.out <- FALSE @@ -325,7 +333,7 @@ q_rsp_plot <- function(spct, s.rsp.label <- expression(Spectral~~photon~~response~~k %*% R[Q~lambda]~~("rel.")) rsp.label.total <- "atop(k %*% R[Q], (\"rel.\"))" rsp.label.avg <- "atop(bar(k %*% R[Q~lambda]), (\"rel.\"))" - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { if (!pc.out) { multiplier.label <- "rel." } else { @@ -342,31 +350,31 @@ q_rsp_plot <- function(spct, warning("Percent scale supported only for normalized cps_spct objects.") pc.out <- FALSE } - time.unit <- getTimeUnit(spct) + time.unit <- photobiology::getTimeUnit(spct) if (!length(time.unit)) { time.unit <- "unkonwn" } time.unit.char <- duration2character(time.unit) - if (time.unit.char=="second") { + if (time.unit.char == "second") { s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~s^{-1}~nm^{-1})) rsp.label.total <- "atop(R[Q], (resp.~~unit~~s^{-1}))" rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~s^{-1}~nm^{-1}))" - } else if (time.unit.char=="day") { + } else if (time.unit.char == "day") { s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~d^{-1}~nm^{-1})) rsp.label.total <- "atop(R[Q], (resp.~~unit~~d^{-1}))" rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~d^{-1}~nm^{-1}))" - } else if (time.unit.char=="hour") { + } else if (time.unit.char == "hour") { s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~~h^{-1}~nm^{-1})) rsp.label.total <- "atop(R[Q], (resp.~~unit~~h^{-1}))" rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~~h^{-1}~nm^{-1}))" - } else if (time.unit.char=="duration") { + } else if (time.unit.char == "duration") { s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~nm^{-1})) rsp.label.total <- "atop(R[Q], (resp.~~unit))" rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~nm^{-1}))" exposure.label <- paste("Length of time:", ifelse(lubridate::is.duration(time.unit), as.character(time.unit), "unknown")) - } else if (time.unit.char=="exposure") { + } else if (time.unit.char == "exposure") { s.rsp.label <- expression(Spectral~~photon~~response~~R[Q~lambda]~~(resp.~~unit~nm^{-1})) rsp.label.total <- "atop(R[Q], (resp.~~unit))" rsp.label.avg <- "atop(bar(R[Q~lambda]), (resp.~~unit~nm^{-1}))" @@ -411,7 +419,8 @@ q_rsp_plot <- function(spct, rsp.label <- "" } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.q.response"]])) + plot <- ggplot2::ggplot(spct, aes(x = .data[["w.length"]], + y = .data[["s.q.response"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -422,26 +431,29 @@ q_rsp_plot <- function(spct, # We want data plotted on top of the boundary lines # Negative response is valid! if ("boundaries" %in% annotations) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "black") } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.rsp.label) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) + plot <- plot + ggplot2::labs(x = expression("Wavelength, "*lambda~(nm)), + y = s.rsp.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- plot + + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() plot <- plot + decoration(w.band = w.band, y.max = y.max, y.min = y.min, - x.max = max(spct), - x.min = min(spct), + x.max = photobiology::wl_max(spct), + x.min = photobiology::wl_min(spct), annotations = annotations, label.qty = label.qty, span = span, @@ -452,12 +464,12 @@ q_rsp_plot <- function(spct, if (!is.na(exposure.label)) { plot <- plot + annotate("text", - x = min(spct), + x = photobiology::wl_min(spct), y = y.max, label = exposure.label, vjust = -0.5, hjust = 0, - size = rel(3), + size = ggplot2::rel(3), na.rm = TRUE ) } @@ -471,23 +483,26 @@ q_rsp_plot <- function(spct, length(intersect(c("boxes", "segments", "labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- + c(photobiology::wl_min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max) - x.limits <- range(spct) + x.limits <- photobiology::wl_range(spct) } if (pc.out) { plot <- plot + - scale_y_continuous(labels = scales::percent, + ggplot2::scale_y_continuous(labels = scales::percent, breaks = y.breaks, limits = y.limits) } else { plot <- - plot + scale_y_continuous(breaks = y.breaks, + plot + ggplot2::scale_y_continuous(breaks = y.breaks, limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } #' Plot one or more response spectra. @@ -517,25 +532,28 @@ q_rsp_plot <- function(spct, #' autoplot(photodiode.spct, geom = "spct") #' autoplot(photodiode.spct, unit.out = "photon") #' autoplot(photodiode.spct, annotations = "") -#' autoplot(photodiode.spct, norm = "skip") -#' autoplot(photodiode.spct, norm = 400) #' #' two_sensors.mspct <- #' response_mspct(list("Photodiode" = photodiode.spct, -#' "Coupled charge device" = ccd.spct)) -#' autoplot(two_sensors.mspct, normalize = TRUE, unit.out = "photon") -#' autoplot(two_sensors.mspct, normalize = TRUE, idfactor = "Spectra") -#' autoplot(two_sensors.mspct, normalize = TRUE, facets = 2) -#' autoplot(two_sensors.mspct, normalize = TRUE, geom = "spct") +#' "Coupled charge device" = ccd.spct)) |> +#' normalize() +#' +#' autoplot(two_sensors.mspct, unit.out = "photon") +#' autoplot(two_sensors.mspct, idfactor = "Spectra") +#' autoplot(two_sensors.mspct, facets = 2) +#' autoplot(two_sensors.mspct, geom = "spct") #' #' @family autoplot methods #' autoplot.response_spct <- function(object, ..., w.band = getOption("photobiology.plot.bands", - default = list(UVC(), UVB(), UVA(), PhR())), + default = list(photobiologyWavebands::UVC(), + photobiologyWavebands::UVB(), + photobiologyWavebands::UVA(), + photobiologyWavebands::PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), @@ -554,13 +572,18 @@ autoplot.response_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (getMultipleWl(object) > 1L && plot.data != "as.is") { + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) + + if (photobiology::getMultipleWl(object) > 1L + && plot.data != "as.is") { return( - autoplot(object = subset2mspct(object), + autoplot(object = photobiology::subset2mspct(object), w.band = w.band, range = range, norm = norm, - unit.out = unit.out, pc.out = pc.out, label.qty = label.qty, span = span, @@ -580,20 +603,17 @@ autoplot.response_spct <- ) } - force(object.label) - force(norm) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "summaries", "colour.guide", "peaks")) annotations <- decode_annotations(annotations, annotations.default) - # normalization updated and base of expression changed in one go - object <- photobiology::normalize(x = object, - range = range, - norm = norm, - unit.out = unit.out, - na.rm = na.rm) + + # Change units if needed, and update normalization + object <- switch(unit.out, + photon = photobiology::e2q(object, action = "replace"), + energy = photobiology::q2e(object, action = "replace")) + if (is.null(label.qty)) { if (photobiology::is_normalized(object) || photobiology::is_scaled(object)) { @@ -612,7 +632,7 @@ autoplot.response_spct <- w.band <- photobiology::waveband(range, wb.name = "Total") } } - if (is.waveband(w.band)) { + if (photobiology::is.waveband(w.band)) { w.band <- list(w.band) } labels <- sapply(w.band, labels)[1, ] @@ -674,8 +694,7 @@ autoplot.response_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default="energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", @@ -685,8 +704,9 @@ autoplot.response_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- photobiology::trim_wl(object, @@ -694,19 +714,11 @@ autoplot.response_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - norm = norm, - unit.out = unit.out, - na.rm = na.rm) - norm <- "skip" - } + # we ensure the units are correct object <- switch(unit.out, - photon = e2q(object, action = "replace"), - energy = q2e(object, action = "replace")) + photon = photobiology::e2q(object, action = "replace"), + energy = photobiology::q2e(object, action = "replace")) # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, @@ -720,26 +732,26 @@ autoplot.response_mspct <- se = photobiology::s_se(object) ) col.name <- c(photon = "s.q.response", energy = "s.e.response") - if (is.response_spct(z) && any(col.name %in% names(z))) { + if (photobiology::is.response_spct(z) && any(col.name %in% names(z))) { autoplot(object = z, range = NULL, norm = norm, unit.out = unit.out, pc.out = pc.out, facets = facets, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z object.label = object.label, na.rm = na.rm, ...) } else { - z <- as.generic_spct(z) + z <- photobiology::as.generic_spct(z) autoplot(object = z, y.name = paste(col.name[unit.out], plot.data, sep = "."), range = NULL, norm = norm, pc.out = pc.out, facets = facets, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z object.label = object.label, na.rm = na.rm, ...) diff --git a/R/autoplot-source-spct.r b/R/autoplot-source-spct.r index 0a2f65b0..c6a67862 100644 --- a/R/autoplot-source-spct.r +++ b/R/autoplot-source-spct.r @@ -61,7 +61,7 @@ e_plot <- function(spct, facets, ylim, na.rm) { - if (!is.source_spct(spct)) { + if (!photobiology::is.source_spct(spct)) { stop("e_plot() can only plot source_spct objects.") } spct[["s.q.irrad"]] <- NULL @@ -73,13 +73,13 @@ e_plot <- function(spct, ylim <- rep(NA_real_, 2L) } if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, range = range(spct)) } duration.label <- NA - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent scale supported only for normalized source_spct objects.") pc.out <- FALSE @@ -88,13 +88,13 @@ e_plot <- function(spct, irrad.label.total <- "atop(k %*% E, (\"rel.\"))" irrad.label.avg <- "atop(bar(E[lambda]), (\"rel.\"))" scale.factor <- 1 - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { if (!pc.out) { multiplier.label <- "rel." } else { multiplier.label <- "%" } - norm <- round(getNormalization(spct)[["norm.wl"]], digits = 1) + norm <- round(photobiology::getNormalization(spct)[["norm.wl"]], digits = 1) s.irrad.label <- bquote(Spectral~~energy~~irradiance~~E[lambda]/E[lambda==.(norm)]~~(.(multiplier.label))) irrad.label.total <- "atop(E, (\"rel.\"))" irrad.label.avg <- bquote(atop(bar(E[lambda]), E[lambda==.(norm)])) @@ -104,7 +104,7 @@ e_plot <- function(spct, warning("Percent scale supported only for normalized source_spct objects.") pc.out <- FALSE } - time.unit <- getTimeUnit(spct) + time.unit <- photobiology::getTimeUnit(spct) if (!length(time.unit)) { time.unit <- "unkonwn" } @@ -159,7 +159,7 @@ e_plot <- function(spct, } else { irrad.label <- "" } - if (is_effective(spct)) { + if (photobiology::is_effective(spct)) { s.irrad.label <- sub("E[lambda]", "E[lambda]^{eff}", s.irrad.label, fixed = TRUE) irrad.label <- sub("E", "E^{eff}", irrad.label, fixed = TRUE) irrad.label.total <- sub("E", "E^{eff}", irrad.label.total, fixed = TRUE) @@ -186,7 +186,9 @@ e_plot <- function(spct, y.max <- max(spct[["s.e.irrad"]], y.min, 0, na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.e.irrad"]])) + plot <- ggplot2::ggplot(spct, + ggplot2::aes(x = .data[["w.length"]], + y = .data[["s.e.irrad"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -197,23 +199,25 @@ e_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.min < (-0.01 * y.max)) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "red") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "black") } } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.irrad.label) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) + plot <- plot + ggplot2::labs(x = expression("Wavelength, "*lambda~(nm)), y = s.irrad.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() if (label.qty == "total") { label.qty <- "irrad" @@ -223,7 +227,7 @@ e_plot <- function(spct, plot <- plot + decoration(w.band = w.band, unit.out = "energy", - time.unit = getTimeUnit(spct), + time.unit = photobiology::getTimeUnit(spct), y.max = y.max, y.min = y.min, x.max = max(spct), @@ -237,24 +241,26 @@ e_plot <- function(spct, chroma.type = chroma.type, na.rm = TRUE) - if (is_effective(spct)) { - plot <- plot + annotate("text", - x = midpoint(spct), - y = y.max, - label = paste("BSWF:", getBSWFUsed(spct)), - vjust = -0.5, size = rel(3), - na.rm = TRUE) + if (photobiology::is_effective(spct)) { + plot <- plot + + ggplot2::annotate("text", + x = photobiology::midpoint(spct), + y = y.max, + label = paste("BSWF:", photobiology::getBSWFUsed(spct)), + vjust = -0.5, size = ggplot2::rel(3), + na.rm = TRUE) } if (!is.na(duration.label)) { - plot <- plot + annotate("text", - x = min(spct), - y = y.max, - label = duration.label, - vjust = -0.5, - hjust = 0, - size = rel(3), - na.rm = TRUE) + plot <- plot + + ggplot2::annotate("text", + x = min(spct), + y = y.max, + label = duration.label, + vjust = -0.5, + hjust = 0, + size = ggplot2::rel(3), + na.rm = TRUE) } if (abs(y.max - 1) < 0.02 && abs(y.min) < 0.02) { @@ -267,7 +273,7 @@ e_plot <- function(spct, length(intersect(c("boxes", "segments", "labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- c(min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max * 1.05) x.limits <- range(spct) @@ -275,15 +281,15 @@ e_plot <- function(spct, if (pc.out) { plot <- plot + - scale_y_continuous(labels = scales::percent, + ggplot2::scale_y_continuous(labels = scales::percent, breaks = y.breaks, limits = y.limits) } else { plot <- - plot + scale_y_continuous(breaks = y.breaks, + plot + ggplot2::scale_y_continuous(breaks = y.breaks, limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + ggplot2::scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) } #' Create a complete ggplot for light-source spectra. @@ -349,7 +355,7 @@ q_plot <- function(spct, facets, ylim, na.rm) { - if (!is.source_spct(spct)) { + if (!photobiology::is.source_spct(spct)) { stop("q_plot() can only plot source_spct objects.") } spct[["s.e.irrad"]] <- NULL @@ -361,14 +367,14 @@ q_plot <- function(spct, ylim <- rep(NA_real_, 2L) } if (!is.null(range)) { - spct <- trim_wl(spct, range = range) + spct <- photobiology::trim_wl(spct, range = range) } if (!is.null(w.band)) { - w.band <- trim_wl(w.band, range = range(spct)) + w.band <- photobiology::trim_wl(w.band, range = range(spct)) } duration.label <- NA - if (is_scaled(spct)) { + if (photobiology::is_scaled(spct)) { if (pc.out) { warning("Percent scale supported only for normalized source_spct objects.") pc.out <- FALSE @@ -377,13 +383,13 @@ q_plot <- function(spct, irrad.label.total <- "atop(k %*% Q, (\"rel.\"))" irrad.label.avg <- "atop(bar(Q[lambda]), (\"rel.\"))" scale.factor <- 1 - } else if (is_normalized(spct)) { + } else if (photobiology::is_normalized(spct)) { if (!pc.out) { multiplier.label <- "rel." } else { multiplier.label <- "%" } - norm <- round(getNormalization(spct)[["norm.wl"]], digits = 1) + norm <- round(photobiology::getNormalization(spct)[["norm.wl"]], digits = 1) s.irrad.label <- bquote(Spectral~~photon~~exposure~~Q[lambda]/Q[lambda==.(norm)]~~(.(multiplier.label))) irrad.label.total <- "atop(Q, (\"rel.\"))" irrad.label.avg <- bquote(atop(bar(Q[lambda]), Q[lambda==.(norm)])) @@ -393,7 +399,7 @@ q_plot <- function(spct, warning("Percent scale supported only for normalized source_spct objects.") pc.out <- FALSE } - time.unit <- getTimeUnit(spct) + time.unit <- photobiology::getTimeUnit(spct) if (!length(time.unit)) { time.unit <- "unkonwn" } @@ -448,7 +454,7 @@ q_plot <- function(spct, } else { irrad.label <- "" } - if (is_effective(spct)) { + if (photobiology::is_effective(spct)) { s.irrad.label <- sub("Q[lambda]", "Q[lambda]^{eff}", s.irrad.label, fixed = TRUE) irrad.label <- sub("Q", "Q^{eff}", irrad.label, fixed = TRUE) irrad.label.total <- sub("Q", "Q^{eff}", irrad.label.total, fixed = TRUE) @@ -475,7 +481,10 @@ q_plot <- function(spct, y.max <- max(spct[["s.q.irrad"]], y.min, 0, na.rm = TRUE) } - plot <- ggplot(spct, aes(x = .data[["w.length"]], y = .data[["s.q.irrad"]])) + plot <- + ggplot2::ggplot(spct, + ggplot2::aes(x = .data[["w.length"]], + y = .data[["s.q.irrad"]])) temp <- find_idfactor(spct = spct, idfactor = idfactor, facets = facets, @@ -486,23 +495,27 @@ q_plot <- function(spct, # We want data plotted on top of the boundary lines if ("boundaries" %in% annotations) { if (y.min < (-0.01 * y.max)) { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "red") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "red") } else { - plot <- plot + geom_hline(yintercept = 0, linetype = "dashed", colour = "black") + plot <- plot + + ggplot2::geom_hline(yintercept = 0, linetype = "dashed", colour = "black") } } if (!is.null(geom) && geom %in% c("area", "spct")) { plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2) } - plot <- plot + geom_line(na.rm = na.rm) - plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.irrad.label) + plot <- plot + ggplot2::geom_line(na.rm = na.rm) + plot <- plot + + ggplot2::labs(x = expression("Wavelength, "*lambda~(nm)), y = s.irrad.label) if (length(annotations) == 1 && annotations == "") { return(plot) } - plot <- plot + scale_fill_identity() + scale_color_identity() + plot <- + plot + ggplot2::scale_fill_identity() + ggplot2::scale_color_identity() if (label.qty == "total") { label.qty <- "irrad" @@ -512,7 +525,7 @@ q_plot <- function(spct, plot <- plot + decoration(w.band = w.band, unit.out = "photon", - time.unit = getTimeUnit(spct), + time.unit = photobiology::getTimeUnit(spct), y.max = y.max, y.min = y.min, x.max = max(spct), @@ -526,24 +539,24 @@ q_plot <- function(spct, chroma.type = chroma.type, na.rm = TRUE) - if (is_effective(spct)) { - plot <- plot + annotate("text", - x = midpoint(spct), - y = y.max, - label = paste("BSWF:", getBSWFUsed(spct)), - vjust = -0.5, size = rel(3), - na.rm = TRUE) + if (photobiology::is_effective(spct)) { + plot <- plot + ggplot2::annotate("text", + x = photobiology::midpoint(spct), + y = y.max, + label = paste("BSWF:", photobiology::getBSWFUsed(spct)), + vjust = -0.5, size = ggplot2::rel(3), + na.rm = TRUE) } if (!is.na(duration.label)) { - plot <- plot + annotate("text", - x = min(spct), - y = y.max, - label = duration.label, - vjust = -0.5, - hjust = 0, - size = rel(3), - na.rm = TRUE) + plot <- plot + ggplot2::annotate("text", + x = min(spct), + y = y.max, + label = duration.label, + vjust = -0.5, + hjust = 0, + size = ggplot2::rel(3), + na.rm = TRUE) } if (abs(y.max - 1) < 0.02 && abs(y.min) < 0.02) { @@ -556,7 +569,7 @@ q_plot <- function(spct, length(intersect(c("boxes", "segments", "labels", "summaries", "colour.guide", "reserve.space"), annotations)) > 0L) { y.limits <- c(y.min, y.min + (y.max - y.min) * 1.25) - x.limits <- c(min(spct) - wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors + x.limits <- c(min(spct) - photobiology::wl_expanse(spct) * 0.025, NA) # NA needed because of rounding errors } else { y.limits <- c(y.min, y.max * 1.05) x.limits <- range(spct) @@ -564,15 +577,16 @@ q_plot <- function(spct, if (pc.out) { plot <- plot + - scale_y_continuous(labels = scales::percent, - breaks = y.breaks, - limits = y.limits) + ggplot2::scale_y_continuous(labels = scales::percent, + breaks = y.breaks, + limits = y.limits) } else { plot <- - plot + scale_y_continuous(breaks = y.breaks, - limits = y.limits) + plot + ggplot2::scale_y_continuous(breaks = y.breaks, + limits = y.limits) } - plot + scale_x_continuous(limits = x.limits, breaks = scales::pretty_breaks(n = 7)) + plot + ggplot2::scale_x_continuous(limits = x.limits, + breaks = scales::pretty_breaks(n = 7)) } #' Plot one or more light-source spectra. @@ -589,11 +603,8 @@ q_plot <- function(spct, #' @param w.band a single waveband object or a list of waveband objects. #' @param range an R object on which \code{range()} returns a vector of length #' 2, with minimum and maximum wavelengths (nm). -#' @param norm numeric Normalization wavelength (nm) or character string -#' \code{"max"}, or \code{"min"} for normalization at the corresponding -#' wavelength, \code{"update"} to update the normalization after modifying -#' units of expression, quantity or range but respecting the previously used -#' criterion, or \code{"skip"} to force return of \code{object} unchanged. +#' @param norm numeric No longer supported, normalization is always updated if +#' present and a unit conversion applied. #' @param unit.out character string indicating type of radiation units to use #' for plotting: \code{"photon"} or its synonym \code{"quantum"}, or #' \code{"energy"}. @@ -673,16 +684,15 @@ q_plot <- function(spct, #' autoplot(sun.spct) #' autoplot(sun.spct, geom = "spct") #' autoplot(sun.spct, unit.out = "photon") -#' autoplot(sun.spct, norm = "max") -#' autoplot(sun.spct, norm = "max", pc.out = TRUE) +#' autoplot(normalize(sun.spct)) +#' autoplot(normalize(sun.spct), pc.out = TRUE) #' #' # multiple spectra in long form #' autoplot(sun_evening.spct) #' autoplot(sun_evening.spct, facets = 1) # one column #' autoplot(sun_evening.spct, facets = 2) # two columns #' autoplot(sun_evening.spct, plot.data = "mean") -#' # needs 'photobiology' (> 0.11.2) -#' # autoplot(sun_evening.spct, idfactor = "Sequence") +#' autoplot(sun_evening.spct, idfactor = "Sequence") #' #' # multiple spectra as a collection #' autoplot(sun_evening.mspct) @@ -701,8 +711,7 @@ autoplot.source_spct <- photobiologyWavebands::UVA(), photobiologyWavebands::PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", - default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), @@ -722,58 +731,49 @@ autoplot.source_spct <- object.label = deparse(substitute(object)), na.rm = TRUE) { - if (is.null(idfactor)) { - idfactor <- getIdFactor(object) - } - if (is.na(idfactor) || !is.character(idfactor)) { - idfactor <- getMultipleWl(object) > 1L - } + force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor) + object <- rename_idfactor(object, idfactor) - if (plot.data != "as.is") { + if (photobiology::getMultipleWl(object) > 1L && plot.data != "as.is") { return( - autoplot(object = subset2mspct(object), - w.band = w.band, - range = range, - norm = norm, - unit.out = unit.out, - pc.out = pc.out, - label.qty = label.qty, - span = span, - wls.target = wls.target, - annotations = annotations, - geom = geom, - time.format = time.format, - tz = tz, - text.size = text.size, - chroma.type = chroma.type, - idfactor = idfactor, - facets = facets, - plot.data = plot.data, - ylim = ylim, - object.label = object.label, - na.rm = na.rm) + ggplot2::autoplot(object = photobiology::subset2mspct(object), + w.band = w.band, + range = range, + unit.out = unit.out, + pc.out = pc.out, + label.qty = label.qty, + span = span, + wls.target = wls.target, + annotations = annotations, + geom = geom, + time.format = time.format, + tz = tz, + text.size = text.size, + chroma.type = chroma.type, + idfactor = idfactor, + facets = facets, + plot.data = plot.data, + ylim = ylim, + object.label = object.label, + na.rm = na.rm) ) } - # support renaming of the idfactor - if (getMultipleWl(object) > 1L && is.character(idfactor) && length(idfactor)) { - setIdFactor(object, idfactor) - } - force(object.label) - annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "summaries", "colour.guide", "peaks")) annotations <- decode_annotations(annotations, annotations.default) - # normalization updated and base of expression changed in one go - object <- normalize(x = object, - range = range, - norm = norm, - unit.out = unit.out, - na.rm = na.rm) + # Change units if needed, and update normalization + object <- switch(unit.out, + photon = photobiology::e2q(object, action = "replace"), + energy = photobiology::q2e(object, action = "replace")) + if (is.null(label.qty)) { - if (is_normalized(object) || is_scaled(object)) { + if (photobiology::is_normalized(object) || + photobiology::is_scaled(object)) { label.qty = "contribution" } else { label.qty = "total" @@ -782,14 +782,14 @@ autoplot.source_spct <- if (length(w.band) == 0) { if (is.null(range)) { - w.band <- waveband(object) - } else if (is.waveband(range)) { + w.band <- photobiology::waveband(object) + } else if (photobiology::is.waveband(range)) { w.band <- range } else { - w.band <- waveband(range, wb.name = "Total") + w.band <- photobiology::waveband(range, wb.name = "Total") } } - if (is.waveband(w.band)) { + if (photobiology::is.waveband(w.band)) { w.band <- list(w.band) } labels <- sapply(w.band, labels)[1, ] @@ -853,8 +853,7 @@ autoplot.source_mspct <- function(object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.normalize", - default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), @@ -865,8 +864,9 @@ autoplot.source_mspct <- na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + idfactor <- check_idfactor_arg(object, idfactor = idfactor, default = TRUE) - idfactor <- validate_idfactor(idfactor = idfactor) # We trim the spectra to avoid unnecessary computations later if (!is.null(range)) { object <- photobiology::trim_wl(object, @@ -874,15 +874,6 @@ autoplot.source_mspct <- use.hinges = TRUE, fill = NULL) } - # We apply the normalization and change of unit to the collection if it is to be bound - # otherwise normalization is applied to the "parallel-summary" spectrum - if (plot.data == "as.is") { - object <- photobiology::normalize(object, - norm = norm, - unit.out = unit.out, - na.rm = na.rm) - norm <- "skip" - } # we ensure the units are correct object <- switch(unit.out, photon = photobiology::e2q(object, action = "replace"), @@ -890,10 +881,7 @@ autoplot.source_mspct <- # we convert the collection of spectra into a single spectrum object # containing a summary spectrum or multiple spectra in long form. z <- switch(plot.data, - as.is = photobiology::rbindspct(object, - idfactor = ifelse(is.na(idfactor), - "spct.idx", - idfactor)), + as.is = photobiology::rbindspct(object, idfactor = idfactor), mean = photobiology::s_mean(object), median = photobiology::s_median(object), sum = photobiology::s_sum(object), @@ -904,13 +892,12 @@ autoplot.source_mspct <- ) col.name <- c(photon = "s.q.irrad", energy = "s.e.irrad") - if (is.source_spct(z) && any(col.name %in% names(z))) { + if (photobiology::is.source_spct(z) && any(col.name %in% names(z))) { ggplot2::autoplot(object = z, range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, unit.out = unit.out, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -920,9 +907,8 @@ autoplot.source_mspct <- ggplot2::autoplot(object = z, y.name = paste(col.name[unit.out], plot.data, sep = "."), range = getOption("ggspectra.wlrange", default = NULL), - norm = norm, pc.out = pc.out, - idfactor = idfactor, + idfactor = NULL, # use idfactor already set in z facets = facets, object.label = object.label, na.rm = na.rm, @@ -930,19 +916,3 @@ autoplot.source_mspct <- } } -## internal - -#' Convert lubridate duration objects to a string if possible -#' -#' @param time.unit lubridate::duration object or character -#' -#' @keywords internal -#' -duration2character <- function(time.unit) { - if (is.character(time.unit)) return(time.unit) - if (!lubridate::is.duration(time.unit)) return("unknown") - if (time.unit == lubridate::duration(1, "seconds")) return("second") - if (time.unit == lubridate::duration(1, "hours")) return("hour") - if (time.unit == lubridate::duration(1, "days")) return("day") - "duration" -} diff --git a/R/autoplot-utils.R b/R/autoplot-utils.R deleted file mode 100644 index 0bf5871e..00000000 --- a/R/autoplot-utils.R +++ /dev/null @@ -1,22 +0,0 @@ -#' Validate idfactor -#' -#' @param idfactor character, logical, NULL or NA. If a \code{character} string, -#' it is validated as an R name, while logical values, NULL and NA are -#' returned unchanged. -#' -#' @keywords internal -#' -validate_idfactor <- function(idfactor) { - if (length(idfactor) > 1L) { - stop("'idfactor' must be of length one or NULL, but is longer") - } - if (!is.null(idfactor) & !is.na(idfactor) & !is.logical(idfactor)) { - idfactor.user <- idfactor - idfactor <- make.names(idfactor) - if (idfactor != idfactor.user) { - message("'idfactor' sanitized from \"", idfactor.user, - "\" into \"", idfactor, "\"") - } - } - idfactor -} diff --git a/R/autoplot-waveband.R b/R/autoplot-waveband.R index 203e0c7a..41a654e2 100644 --- a/R/autoplot-waveband.R +++ b/R/autoplot-waveband.R @@ -23,8 +23,8 @@ #' \code{character} strings "half.maximum" and "half.range" are also accepted #' as arguments. A list with \code{numeric} and/or \code{character} values is #' also accepted. -#' @param unit.in the type of unit we assume as reference "energy" or "photon" -#' based. +#' @param unit.in,unit.out the type of unit we assume as reference "energy" or +#' "photon" based. #' @param annotations a character vector. For details please see section Plot #' Annotations. #' @param geom character The name of a ggplot geometry, currently only @@ -76,26 +76,25 @@ autoplot.waveband <- span = NULL, wls.target = "HM", unit.in = getOption("photobiology.radiation.unit", default = "energy"), + unit.out = unit.in, annotations = NULL, geom = "line", wb.trim = TRUE, - norm = NULL, + norm = NA, text.size = 2.5, ylim = c(NA, NA), object.label = deparse(substitute(object)), na.rm = TRUE) { force(object.label) + warn_norm_arg(norm) + w.band <- object annotations.default <- getOption("photobiology.plot.annotations", default = c("boxes", "labels", "colour.guide")) annotations <- c("=", decode_annotations(annotations, annotations.default)) - w.band <- object - if (!is.waveband(w.band)) { - return(ggplot()) - } if (!is.null(w.length)) { w.length <- unique(sort(w.length, na.last = NA)) } @@ -123,13 +122,6 @@ autoplot.waveband <- unit.out = unit.in, unit.in = unit.in, use.cached.mult = getOption("photobiology.use.cached.mult", default = FALSE), fill = fill) - if (is.null(norm)) { - if (!is.null(w.band$norm)) { - norm <- w.band$norm - } else { - norm <- "max" - } - } if (unit.in == "energy") { spct <- response_spct(w.length = w.length, s.e.response = s.response) } else if (unit.in %in% c("photon", "quantum")) { @@ -149,10 +141,10 @@ autoplot.waveband <- wb.trim = wb.trim, span = span, wls.target = wls.target, - norm = norm, text.size = text.size, ylim = ylim, na.rm = na.rm, + unit.out = unit.out, ...) + autotitle(object = object, object.label = object.label, diff --git a/R/autotitle.R b/R/autotitle.R index 0f3352ba..d1e06d38 100644 --- a/R/autotitle.R +++ b/R/autotitle.R @@ -61,6 +61,7 @@ autotitle <- function(object, tz = "", default.title = "title:objt") { + force(object.label) if (!is.character(object.label)) { if (is.name(object.label)) { object.label <- as.character(object.label) diff --git a/R/axis-utils-calibration-spct.R b/R/axis-utils-calibration-spct.R index 097f0ec3..3d4dadae 100644 --- a/R/axis-utils-calibration-spct.R +++ b/R/axis-utils-calibration-spct.R @@ -49,7 +49,10 @@ multipliers_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "k(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $k_{\\lambda} / k_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -125,7 +128,9 @@ scale_y_multipliers_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -136,7 +141,7 @@ scale_y_multipliers_continuous <- axis.symbols = getOption("ggspectra.axis.symbols", default = TRUE), ...) { - scale_y_continuous(name = name, - labels = labels, - ...) + ggplot2::scale_y_continuous(name = name, + labels = labels, + ...) } diff --git a/R/axis-utils-cps-spct.R b/R/axis-utils-cps-spct.R index 76b88337..d9890c8f 100644 --- a/R/axis-utils-cps-spct.R +++ b/R/axis-utils-cps-spct.R @@ -49,7 +49,10 @@ cps_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "n(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " rate $n_{\\lambda} / N_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -137,16 +140,29 @@ cps_label <- function(unit.exponent = 0, #' #' ggplot(norm_led.cps_spct) + #' geom_line() + +#' scale_y_cps_continuous(normalized = is_normalized(norm_led.cps_spct)) + +#' scale_x_wl_continuous() +#' +#' ggplot(norm_led.cps_spct) + +#' geom_line() + #' scale_y_cps_continuous(normalized = getNormalized(norm_led.cps_spct)) + #' scale_x_wl_continuous() #' +#' ggplot(norm_led.cps_spct) + +#' geom_line() + +#' scale_y_cps_continuous(normalized = +#' normalization(norm_led.cps_spct)$norm.type) + +#' scale_x_wl_continuous() +#' scale_y_cps_continuous <- function(unit.exponent = 0, name = cps_label(unit.exponent = unit.exponent, format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", diff --git a/R/axis-utils-filter-spct.R b/R/axis-utils-filter-spct.R index 9e8b9396..b9f621b9 100644 --- a/R/axis-utils-filter-spct.R +++ b/R/axis-utils-filter-spct.R @@ -62,7 +62,10 @@ A_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, " A(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $A_{\\lambda}/A_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -217,13 +220,20 @@ A_total_label <- function(unit.exponent = 0, #' scale_y_A_total_continuous(axis.symbols = FALSE) + #' scale_x_wl_continuous(axis.symbols = FALSE) #' +#' ggplot(yellow_gel.spct, plot.qty = "absorbance") + +#' geom_line() + +#' scale_y_A_internal_continuous(normalized = "none") + +#' scale_x_wl_continuous() +#' scale_y_A_continuous <- function(unit.exponent = 0, name = A_label(unit.exponent = unit.exponent, format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = Tfr.type), labels = SI_pl_format(exponent = unit.exponent), @@ -251,7 +261,9 @@ scale_y_A_internal_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "internal"), labels = SI_pl_format(exponent = unit.exponent), @@ -278,7 +290,9 @@ scale_y_A_total_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "total"), labels = SI_pl_format(exponent = unit.exponent), @@ -378,7 +392,10 @@ Tfr_label <- function(unit.exponent = ifelse(pc.out, -2, 0), } else if (format == "R.character") { paste(label.text, " t(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $\\tau_{\\lambda}/\\tau_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -530,29 +547,37 @@ Tfr_total_label <- function(unit.exponent = 0, #' scale_y_Tfr_total_continuous(axis.symbols = FALSE) + #' scale_x_wl_continuous(axis.symbols = FALSE) #' +#' ggplot(normalize(yellow_gel.spct)) + +#' geom_line() + +#' scale_y_Tfr_total_continuous(normalized = "max") + +#' scale_x_wl_continuous() +#' #' unset_filter_qty_default() #' -scale_y_Tfr_continuous <- function(unit.exponent = ifelse(pc.out, -2, 0), - name = Tfr_label(unit.exponent = unit.exponent, - format = format, - label.text = label.text, - scaled = scaled, - normalized = round(normalized, 1), - axis.symbols = axis.symbols, - Tfr.type = Tfr.type), - labels = SI_pl_format(exponent = unit.exponent), - limits = c(0, 1), - format = getOption("photobiology.math", - default = "R.expression"), - label.text = NULL, - scaled = FALSE, - normalized = FALSE, - axis.symbols = getOption("ggspectra.axis.symbols", - default = TRUE), - pc.out = getOption("ggspectra.pc.out", - default = FALSE), - Tfr.type, - ...) { +scale_y_Tfr_continuous <- + function(unit.exponent = ifelse(pc.out, -2, 0), + name = Tfr_label(unit.exponent = unit.exponent, + format = format, + label.text = label.text, + scaled = scaled, + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), + axis.symbols = axis.symbols, + Tfr.type = Tfr.type), + labels = SI_pl_format(exponent = unit.exponent), + limits = c(0, 1), + format = getOption("photobiology.math", + default = "R.expression"), + label.text = NULL, + scaled = FALSE, + normalized = FALSE, + axis.symbols = getOption("ggspectra.axis.symbols", + default = TRUE), + pc.out = getOption("ggspectra.pc.out", + default = FALSE), + Tfr.type, + ...) { scale_y_continuous(name = name, labels = labels, limits = limits, @@ -569,7 +594,9 @@ scale_y_Tfr_internal_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "internal"), labels = SI_pl_format(exponent = unit.exponent), @@ -600,7 +627,9 @@ scale_y_Tfr_total_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "total"), labels = SI_pl_format(exponent = unit.exponent), @@ -888,7 +917,10 @@ Rfr_label <- function(unit.exponent = ifelse(pc.out, -2, 0), } else if (format == "R.character") { paste(label.text, " r (lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $\\rho_{\\lambda}/\\rho_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -1042,13 +1074,21 @@ Rfr_total_label <- function(unit.exponent = ifelse(pc.out, -2, 0), #' scale_y_Rfr_specular_continuous(axis.symbols = FALSE) + #' scale_x_wl_continuous(axis.symbols = FALSE) #' +#' ggplot(normalize(Ler_leaf_rflt.spct)) + +#' geom_line() + +#' scale_y_Rfr_continuous(Rfr.type = getRfrType(Ler_leaf_rflt.spct), +#' normalized = "max") + +#' scale_x_wl_continuous() +#' scale_y_Rfr_continuous <- function(unit.exponent = ifelse(pc.out, -2, 0), name = Rfr_label(unit.exponent = unit.exponent, format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Rfr.type = Rfr.type), labels = SI_pl_format(exponent = unit.exponent), @@ -1080,7 +1120,9 @@ scale_y_Rfr_specular_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Rfr.type = "specular"), labels = SI_pl_format(exponent = unit.exponent), @@ -1111,7 +1153,9 @@ scale_y_Rfr_total_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Rfr.type = "total"), labels = SI_pl_format(exponent = unit.exponent), diff --git a/R/axis-utils-raw-spct.R b/R/axis-utils-raw-spct.R index f1042162..77ec23f0 100644 --- a/R/axis-utils-raw-spct.R +++ b/R/axis-utils-raw-spct.R @@ -47,7 +47,10 @@ counts_label <- function(unit.exponent = 3, } else if (format == "R.character") { "Pixel response N(lambda) (rel. units)" } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $N_{\\lambda} / N_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -137,16 +140,11 @@ counts_label <- function(unit.exponent = 3, #' scale_y_counts_tg_continuous(unit.exponent = 0) + #' scale_x_wl_continuous() #' -#' norm_led.raw_spct <- normalize(white_led.raw_spct[ , 1:2], norm = "max") -#' -#' ggplot(norm_led.raw_spct) + -#' geom_line() + -#' scale_y_counts_continuous(normalized = getNormalized(norm_led.raw_spct)) + -#' scale_x_wl_continuous() +#' norm_led.raw_spct <- normalize(white_led.raw_spct, norm = "max") #' #' ggplot(norm_led.raw_spct) + #' geom_line() + -#' scale_y_counts_tg_continuous(normalized = getNormalized(norm_led.raw_spct)) + +#' scale_y_counts_continuous(unit.exponent = 0, normalized = "max") + #' scale_x_wl_continuous() #' scale_y_counts_continuous <- @@ -155,7 +153,9 @@ scale_y_counts_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -181,7 +181,9 @@ scale_y_counts_tg_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_tg_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -192,7 +194,7 @@ scale_y_counts_tg_continuous <- axis.symbols = getOption("ggspectra.axis.symbols", default = TRUE), ...) { - scale_y_continuous(name = name, - labels = labels, - ...) + ggplot2::scale_y_continuous(name = name, + labels = labels, + ...) } diff --git a/R/axis-utils-response-spct.R b/R/axis-utils-response-spct.R index 4d003f2c..6e8d5362 100644 --- a/R/axis-utils-response-spct.R +++ b/R/axis-utils-response-spct.R @@ -64,7 +64,10 @@ s.e.response_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "R(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $R(E)_{\\lambda} / R(E)_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -141,7 +144,10 @@ s.q.response_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, " (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $R(Q)_{\\lambda} / R(Q)_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -218,7 +224,10 @@ s.e.action_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "A(E)(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $A(E)_{\\lambda} / A(E)_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -295,7 +304,10 @@ s.q.action_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "A(Q)(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $A(Q)_{\\lambda} / A(Q)_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -400,6 +412,12 @@ s.q.action_label <- function(unit.exponent = 0, #' scale_y_s.e.response_continuous(normalized = getNormalized(norm_ccd.spct)) + #' scale_x_wl_continuous() #' +#' ggplot(norm_ccd.spct) + +#' geom_line() + +#' scale_y_s.e.response_continuous(normalized = +#' normalization(norm_ccd.spct)$norm.type) + +#' scale_x_wl_continuous() +#' #' photon_as_default() #' #' norm_ccd.spct <- normalize(ccd.spct, norm = "max") @@ -422,7 +440,9 @@ scale_y_s.e.response_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), # per unit format = getOption("photobiology.math", @@ -448,7 +468,9 @@ scale_y_s.q.response_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), # per unit format = getOption("photobiology.math", @@ -474,7 +496,9 @@ scale_y_s.e.action_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), # per unit format = getOption("photobiology.math", @@ -500,7 +524,9 @@ scale_y_s.q.action_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), # per unit format = getOption("photobiology.math", diff --git a/R/axis-utils-source-spct.R b/R/axis-utils-source-spct.R index 16eb723b..14ae6407 100644 --- a/R/axis-utils-source-spct.R +++ b/R/axis-utils-source-spct.R @@ -54,7 +54,10 @@ s.e.irrad_label <- function(unit.exponent = 0, } else if (format == "R.character") { paste(label.text, "E(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $E_{\\lambda} / E_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -131,7 +134,10 @@ s.q.irrad_label <- function(unit.exponent = ifelse(normalized, 0, -6), } else if (format == "R.character") { paste(label.text, "Q(lambda) (rel. units)") } - } else if (normalized) { + } else if (is.character(normalized) || normalized) { + if (is.logical(normalized)) { + normalized <- "norm" + } if (tolower(format) == "latex") { paste(label.text, " $Q_{\\lambda} / Q_{", normalized, "}$ (/1)", sep = "") } else if (format == "R.expression") { @@ -238,11 +244,17 @@ s.q.irrad_label <- function(unit.exponent = ifelse(normalized, 0, -6), #' scale_x_wl_continuous() #' #' photon_as_default() -#' normalized_sun.spct <- normalize(sun.spct) +#' normalized_sun.spct <- normalize(e2q(sun.spct, action = "replace")) +#' ggplot(normalized_sun.spct) + +#' geom_line(na.rm = TRUE) + +#' scale_y_s.q.irrad_continuous(normalized = +#' normalization(normalized_sun.spct)$norm.wl) + +#' scale_x_wl_continuous() +#' #' ggplot(normalized_sun.spct) + #' geom_line(na.rm = TRUE) + #' scale_y_s.q.irrad_continuous(normalized = -#' getNormalized(normalized_sun.spct)) + +#' normalization(normalized_sun.spct)$norm.type) + #' scale_x_wl_continuous() #' #' unset_radiation_unit_default() @@ -253,7 +265,9 @@ scale_y_s.e.irrad_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -279,7 +293,9 @@ scale_y_s.q.irrad_continuous <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -305,7 +321,9 @@ scale_y_s.e.irrad_log10 <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -331,7 +349,9 @@ scale_y_s.q.irrad_log10 <- format = format, label.text = label.text, scaled = scaled, - normalized = round(normalized, 1), + normalized = ifelse(is.numeric(normalized), + round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", @@ -347,20 +367,3 @@ scale_y_s.q.irrad_log10 <- ...) } -## internal - -#' Convert lubridate duration objects to a string if possible -#' -#' @param time.unit lubridate::duration object or character -#' -#' @keywords internal -#' -duration2character <- function(time.unit) { - if (is.character(time.unit)) return(time.unit) - if (!lubridate::is.duration(time.unit)) return("unknown") - if (time.unit == lubridate::duration(1, "seconds")) return("second") - if (time.unit == lubridate::duration(1, "hours")) return("hour") - if (time.unit == lubridate::duration(1, "days")) return("day") - "duration" -} - diff --git a/R/utils-internal.R b/R/utils-internal.R new file mode 100644 index 00000000..4ef2f67e --- /dev/null +++ b/R/utils-internal.R @@ -0,0 +1,69 @@ +## internal + +#' Check idfactor argument and retrieve if needed +#' +#' @param object generic_spct object. +#' @param idfactor character, NULL or NA The name of the factor identifying +#' spectra when stored in long form. +#' +#' @keywords internal +#' +check_idfactor_arg <- function(object, idfactor = NULL, default = FALSE) { + if (length(idfactor) > 1L) { + warning("Length of 'idfactor' > 1, using: '", idfactor[1], "',") + idfactor <- idfactor[1] + } + if (is.null(idfactor) || is.na(idfactor)) { + idfactor <- photobiology::getIdFactor(object) + } + if (is.na(idfactor) || !is.character(idfactor)) { + idfactor <- default || photobiology::getMultipleWl(object) > 1L + } + idfactor +} + +#' Update idfactor name in object +#' +#' @param object generic_spct object. +#' @param idfactor character The name of the factor identifying spectra when +#' stored in long form. +#' +#' @keywords internal +#' +rename_idfactor <- function(object, idfactor) { + if (is.character(idfactor) && + photobiology::getIdFactor(object) != idfactor) { + object <- photobiology::setIdFactor(object, idfactor = idfactor) + } + object +} + + +#' Convert lubridate duration objects to a string if possible +#' +#' @param time.unit lubridate::duration object or character +#' +#' @keywords internal +#' +duration2character <- function(time.unit) { + if (is.character(time.unit)) return(time.unit) + if (!lubridate::is.duration(time.unit)) return("unknown") + if (time.unit == lubridate::duration(1, "seconds")) return("second") + if (time.unit == lubridate::duration(1, "hours")) return("hour") + if (time.unit == lubridate::duration(1, "days")) return("day") + "duration" +} + +#' Warn if norm argument passed in call +#' +#' @param norm numeric or character No longer supported, normalization is always +#' updated in \code{autoplot()} if present and a unit conversion applied. +#' +#' @keywords internal +#' +warn_norm_arg <- function(norm) { + if (!is.na(norm)) { + warning("On-the-fly normalization no longer supported. Use 'normalize()' instead.") + } +} + diff --git a/ggspectra.Rproj b/ggspectra.Rproj index 9625dd1f..2a7d214c 100644 --- a/ggspectra.Rproj +++ b/ggspectra.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: d28d46dd-d639-4847-aabb-b4b205390f38 RestoreWorkspace: No SaveWorkspace: No diff --git a/man/autoplot.calibration_spct.Rd b/man/autoplot.calibration_spct.Rd index 3fbf98cc..e54f939d 100644 --- a/man/autoplot.calibration_spct.Rd +++ b/man/autoplot.calibration_spct.Rd @@ -20,7 +20,7 @@ geom = "line", time.format = "", tz = "UTC", - norm = NULL, + norm = NA, text.size = 2.5, idfactor = NULL, facets = FALSE, @@ -35,7 +35,7 @@ ..., range = getOption("ggspectra.wlrange", default = NULL), unit.out = "ignored", - norm = getOption("ggspectra.normalize", default = "skip"), + norm = NA, pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", idfactor = TRUE, @@ -86,11 +86,8 @@ selects between them based on \code{stacked}.} \item{tz}{character Time zone to use for title and/or subtitle.} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{text.size}{numeric size of text in the plot decorations.} diff --git a/man/autoplot.cps_spct.Rd b/man/autoplot.cps_spct.Rd index a73aec9a..ef3adc3a 100644 --- a/man/autoplot.cps_spct.Rd +++ b/man/autoplot.cps_spct.Rd @@ -11,7 +11,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, unit.out = NULL, pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = "mean", @@ -55,11 +55,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{unit.out}{character IGNORED.} diff --git a/man/autoplot.filter_spct.Rd b/man/autoplot.filter_spct.Rd index aa8a97f4..473d985e 100644 --- a/man/autoplot.filter_spct.Rd +++ b/man/autoplot.filter_spct.Rd @@ -11,7 +11,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "transmittance"), pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = NULL, @@ -35,7 +35,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "transmittance"), pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", @@ -56,11 +56,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{plot.qty}{character string one of "transmittance" or "absorbance".} @@ -197,13 +194,13 @@ The plotting of absorbance is an exception to scale limits as the autoplot(yellow_gel.spct) autoplot(yellow_gel.spct, geom = "spct") autoplot(yellow_gel.spct, plot.qty = "transmittance") -autoplot(yellow_gel.spct, plot.qty = "absorptance") autoplot(yellow_gel.spct, plot.qty = "absorbance") autoplot(yellow_gel.spct, pc.out = TRUE) autoplot(yellow_gel.spct, annotations = c("+", "wls")) # spectra for two filters in long form autoplot(two_filters.spct) +autoplot(two_filters.spct, idfactor = TRUE) autoplot(two_filters.spct, idfactor = "Spectra") autoplot(two_filters.spct, facets = TRUE) diff --git a/man/autoplot.generic_spct.Rd b/man/autoplot.generic_spct.Rd index daa43bad..bdefd820 100644 --- a/man/autoplot.generic_spct.Rd +++ b/man/autoplot.generic_spct.Rd @@ -15,6 +15,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), + norm = NA, label.qty = "none", span = NULL, wls.target = "HM", @@ -47,6 +48,9 @@ to the y aesthetic.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} + \item{label.qty}{character string giving the type of summary quantity to use for labels, one of \code{"mean"}, \code{"total"}, \code{"contribution"}, and \code{"relative"}.} @@ -155,6 +159,7 @@ If \code{idfactor = NULL}, the default for single spectra, the name of sun.generic_spct <- as.generic_spct(sun.spct) autoplot(sun.generic_spct, y.name = "s.q.irrad") +autoplot(sun.generic_spct, y.name = "s.e.irrad") autoplot(sun.generic_spct, y.name = "s.q.irrad", annotations = "") autoplot(sun.generic_spct, y.name = "s.q.irrad", diff --git a/man/autoplot.object_spct.Rd b/man/autoplot.object_spct.Rd index a80497be..11ddf325 100644 --- a/man/autoplot.object_spct.Rd +++ b/man/autoplot.object_spct.Rd @@ -11,7 +11,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, plot.qty = "all", pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = NULL, @@ -36,7 +36,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = "skip", + norm = NA, plot.qty = getOption("photobiology.filter.qty", default = "all"), pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", @@ -57,11 +57,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{plot.qty}{character string, one of "all", "transmittance", "absorbance", "absorptance", or "reflectance".} diff --git a/man/autoplot.raw_spct.Rd b/man/autoplot.raw_spct.Rd index 0c1d129b..3c5baab3 100644 --- a/man/autoplot.raw_spct.Rd +++ b/man/autoplot.raw_spct.Rd @@ -11,6 +11,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), + norm = NA, unit.out = "counts", pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = "mean", @@ -20,7 +21,6 @@ geom = "line", time.format = "", tz = "UTC", - norm = "skip", text.size = 2.5, idfactor = NULL, facets = FALSE, @@ -34,7 +34,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "skip"), + norm = NA, unit.out = "counts", pc.out = getOption("ggspectra.pc.out", default = FALSE), idfactor = TRUE, @@ -55,6 +55,9 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} + \item{unit.out}{character IGNORED.} \item{pc.out}{logical, if \code{TRUE} use percent instead of fraction of one @@ -86,12 +89,6 @@ selects between them based on \code{stacked}.} \item{tz}{character Time zone to use for title and/or subtitle.} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} - \item{text.size}{numeric size of text in the plot decorations.} \item{idfactor}{character Name of an index column in data holding a diff --git a/man/autoplot.reflector_spct.Rd b/man/autoplot.reflector_spct.Rd index e9382444..5454978b 100644 --- a/man/autoplot.reflector_spct.Rd +++ b/man/autoplot.reflector_spct.Rd @@ -11,7 +11,7 @@ w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, plot.qty = getOption("photobiology.reflector.qty", default = "reflectance"), pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = NULL, @@ -35,7 +35,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.normalize", default = "update"), + norm = NA, plot.qty = getOption("photobiology.reflector.qty", default = "reflectance"), pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", @@ -56,11 +56,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{plot.qty}{character string (currently ignored).} diff --git a/man/autoplot.response_spct.Rd b/man/autoplot.response_spct.Rd index 9bbabb16..26d6189b 100644 --- a/man/autoplot.response_spct.Rd +++ b/man/autoplot.response_spct.Rd @@ -8,10 +8,11 @@ \method{autoplot}{response_spct}( object, ..., - w.band = getOption("photobiology.plot.bands", default = list(UVC(), UVB(), UVA(), - PhR())), + w.band = getOption("photobiology.plot.bands", default = + list(photobiologyWavebands::UVC(), photobiologyWavebands::UVB(), + photobiologyWavebands::UVA(), photobiologyWavebands::PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = NULL, @@ -34,7 +35,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), plot.data = "as.is", @@ -55,11 +56,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{unit.out}{character string indicating type of radiation units to use for plotting: \code{"photon"} or its synonym \code{"quantum"}, or @@ -188,16 +186,16 @@ autoplot(photodiode.spct) autoplot(photodiode.spct, geom = "spct") autoplot(photodiode.spct, unit.out = "photon") autoplot(photodiode.spct, annotations = "") -autoplot(photodiode.spct, norm = "skip") -autoplot(photodiode.spct, norm = 400) two_sensors.mspct <- response_mspct(list("Photodiode" = photodiode.spct, - "Coupled charge device" = ccd.spct)) -autoplot(two_sensors.mspct, normalize = TRUE, unit.out = "photon") -autoplot(two_sensors.mspct, normalize = TRUE, idfactor = "Spectra") -autoplot(two_sensors.mspct, normalize = TRUE, facets = 2) -autoplot(two_sensors.mspct, normalize = TRUE, geom = "spct") + "Coupled charge device" = ccd.spct)) |> + normalize() + +autoplot(two_sensors.mspct, unit.out = "photon") +autoplot(two_sensors.mspct, idfactor = "Spectra") +autoplot(two_sensors.mspct, facets = 2) +autoplot(two_sensors.mspct, geom = "spct") } \seealso{ diff --git a/man/autoplot.source_spct.Rd b/man/autoplot.source_spct.Rd index 188d6c10..0085f6cf 100644 --- a/man/autoplot.source_spct.Rd +++ b/man/autoplot.source_spct.Rd @@ -12,7 +12,7 @@ list(photobiologyWavebands::UVC(), photobiologyWavebands::UVB(), photobiologyWavebands::UVA(), photobiologyWavebands::PhR())), range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.norm", default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), label.qty = NULL, @@ -36,7 +36,7 @@ object, ..., range = getOption("ggspectra.wlrange", default = NULL), - norm = getOption("ggspectra.normalize", default = "update"), + norm = NA, unit.out = getOption("photobiology.radiation.unit", default = "energy"), pc.out = getOption("ggspectra.pc.out", default = FALSE), idfactor = TRUE, @@ -57,11 +57,8 @@ to the plot methods for individual spectra, otherwise currently ignored.} \item{range}{an R object on which \code{range()} returns a vector of length 2, with minimum and maximum wavelengths (nm).} -\item{norm}{numeric Normalization wavelength (nm) or character string -\code{"max"}, or \code{"min"} for normalization at the corresponding -wavelength, \code{"update"} to update the normalization after modifying -units of expression, quantity or range but respecting the previously used -criterion, or \code{"skip"} to force return of \code{object} unchanged.} +\item{norm}{numeric No longer supported, normalization is always updated if +present and a unit conversion applied.} \item{unit.out}{character string indicating type of radiation units to use for plotting: \code{"photon"} or its synonym \code{"quantum"}, or @@ -191,16 +188,15 @@ If \code{idfactor = NULL}, the default for single spectra, the name of autoplot(sun.spct) autoplot(sun.spct, geom = "spct") autoplot(sun.spct, unit.out = "photon") -autoplot(sun.spct, norm = "max") -autoplot(sun.spct, norm = "max", pc.out = TRUE) +autoplot(normalize(sun.spct)) +autoplot(normalize(sun.spct), pc.out = TRUE) # multiple spectra in long form autoplot(sun_evening.spct) autoplot(sun_evening.spct, facets = 1) # one column autoplot(sun_evening.spct, facets = 2) # two columns autoplot(sun_evening.spct, plot.data = "mean") -# needs 'photobiology' (> 0.11.2) -# autoplot(sun_evening.spct, idfactor = "Sequence") +autoplot(sun_evening.spct, idfactor = "Sequence") # multiple spectra as a collection autoplot(sun_evening.mspct) diff --git a/man/autoplot.waveband.Rd b/man/autoplot.waveband.Rd index cab79e27..135c16cc 100644 --- a/man/autoplot.waveband.Rd +++ b/man/autoplot.waveband.Rd @@ -13,10 +13,11 @@ span = NULL, wls.target = "HM", unit.in = getOption("photobiology.radiation.unit", default = "energy"), + unit.out = unit.in, annotations = NULL, geom = "line", wb.trim = TRUE, - norm = NULL, + norm = NA, text.size = 2.5, ylim = c(NA, NA), object.label = deparse(substitute(object)), @@ -46,8 +47,8 @@ which wavelengths are to be searched and interpolated if need. The as arguments. A list with \code{numeric} and/or \code{character} values is also accepted.} -\item{unit.in}{the type of unit we assume as reference "energy" or "photon" -based.} +\item{unit.in, unit.out}{the type of unit we assume as reference "energy" or +"photon" based.} \item{annotations}{a character vector. For details please see section Plot Annotations.} diff --git a/man/check_idfactor_arg.Rd b/man/check_idfactor_arg.Rd new file mode 100644 index 00000000..1d548e9c --- /dev/null +++ b/man/check_idfactor_arg.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils-internal.R +\name{check_idfactor_arg} +\alias{check_idfactor_arg} +\title{Check idfactor argument and retrieve if needed} +\usage{ +check_idfactor_arg(object, idfactor = NULL, default = FALSE) +} +\arguments{ +\item{object}{generic_spct object.} + +\item{idfactor}{character, NULL or NA The name of the factor identifying +spectra when stored in long form.} +} +\description{ +Check idfactor argument and retrieve if needed +} +\keyword{internal} diff --git a/man/duration2character.Rd b/man/duration2character.Rd index e6270edb..f4144a84 100644 --- a/man/duration2character.Rd +++ b/man/duration2character.Rd @@ -1,20 +1,15 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/autoplot-source-spct.r, -% R/axis-utils-source-spct.R +% Please edit documentation in R/utils-internal.R \name{duration2character} \alias{duration2character} \title{Convert lubridate duration objects to a string if possible} \usage{ -duration2character(time.unit) - duration2character(time.unit) } \arguments{ \item{time.unit}{lubridate::duration object or character} } \description{ -Convert lubridate duration objects to a string if possible - Convert lubridate duration objects to a string if possible } \keyword{internal} diff --git a/man/raw_plot.Rd b/man/raw_plot.Rd index b45000ba..015701b9 100644 --- a/man/raw_plot.Rd +++ b/man/raw_plot.Rd @@ -14,7 +14,6 @@ raw_plot( wls.target, annotations, geom, - relative, text.size, idfactor, facets, diff --git a/man/rename_idfactor.Rd b/man/rename_idfactor.Rd new file mode 100644 index 00000000..89a0e1d3 --- /dev/null +++ b/man/rename_idfactor.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils-internal.R +\name{rename_idfactor} +\alias{rename_idfactor} +\title{Update idfactor name in object} +\usage{ +rename_idfactor(object, idfactor) +} +\arguments{ +\item{object}{generic_spct object.} + +\item{idfactor}{character The name of the factor identifying spectra when +stored in long form.} +} +\description{ +Update idfactor name in object +} +\keyword{internal} diff --git a/man/scale_y_A_continuous.Rd b/man/scale_y_A_continuous.Rd index 006fd7ee..2adffbd1 100644 --- a/man/scale_y_A_continuous.Rd +++ b/man/scale_y_A_continuous.Rd @@ -9,8 +9,8 @@ scale_y_A_continuous( unit.exponent = 0, name = A_label(unit.exponent = unit.exponent, format = format, label.text = label.text, - scaled = scaled, normalized = round(normalized, 1), axis.symbols = axis.symbols, - Tfr.type = Tfr.type), + scaled = scaled, normalized = ifelse(is.numeric(normalized), round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = Tfr.type), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = NULL, @@ -24,8 +24,8 @@ scale_y_A_continuous( scale_y_A_internal_continuous( unit.exponent = 0, name = A_label(unit.exponent = unit.exponent, format = format, label.text = label.text, - scaled = scaled, normalized = round(normalized, 1), axis.symbols = axis.symbols, - Tfr.type = "internal"), + scaled = scaled, normalized = ifelse(is.numeric(normalized), round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "internal"), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = NULL, @@ -38,8 +38,8 @@ scale_y_A_internal_continuous( scale_y_A_total_continuous( unit.exponent = 0, name = A_label(unit.exponent = unit.exponent, format = format, label.text = label.text, - scaled = scaled, normalized = round(normalized, 1), axis.symbols = axis.symbols, - Tfr.type = "total"), + scaled = scaled, normalized = ifelse(is.numeric(normalized), round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols, Tfr.type = "total"), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = NULL, @@ -102,4 +102,9 @@ ggplot(yellow_gel.spct, plot.qty = "absorbance") + scale_y_A_total_continuous(axis.symbols = FALSE) + scale_x_wl_continuous(axis.symbols = FALSE) +ggplot(yellow_gel.spct, plot.qty = "absorbance") + + geom_line() + + scale_y_A_internal_continuous(normalized = "none") + + scale_x_wl_continuous() + } diff --git a/man/scale_y_Rfr_continuous.Rd b/man/scale_y_Rfr_continuous.Rd index fa371667..6d354cc3 100644 --- a/man/scale_y_Rfr_continuous.Rd +++ b/man/scale_y_Rfr_continuous.Rd @@ -9,8 +9,9 @@ scale_y_Rfr_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Rfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Rfr.type = Rfr.type), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Rfr.type = + Rfr.type), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -26,8 +27,9 @@ scale_y_Rfr_continuous( scale_y_Rfr_specular_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Rfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Rfr.type = "specular"), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Rfr.type = + "specular"), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -42,8 +44,9 @@ scale_y_Rfr_specular_continuous( scale_y_Rfr_total_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Rfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Rfr.type = "total"), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Rfr.type = + "total"), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -122,4 +125,10 @@ ggplot(Ler_leaf_rflt.spct) + scale_y_Rfr_specular_continuous(axis.symbols = FALSE) + scale_x_wl_continuous(axis.symbols = FALSE) +ggplot(normalize(Ler_leaf_rflt.spct)) + + geom_line() + + scale_y_Rfr_continuous(Rfr.type = getRfrType(Ler_leaf_rflt.spct), + normalized = "max") + + scale_x_wl_continuous() + } diff --git a/man/scale_y_Tfr_continuous.Rd b/man/scale_y_Tfr_continuous.Rd index 836d863f..24291009 100644 --- a/man/scale_y_Tfr_continuous.Rd +++ b/man/scale_y_Tfr_continuous.Rd @@ -9,8 +9,9 @@ scale_y_Tfr_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Tfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Tfr.type = Tfr.type), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Tfr.type = + Tfr.type), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -26,8 +27,9 @@ scale_y_Tfr_continuous( scale_y_Tfr_internal_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Tfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Tfr.type = "internal"), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Tfr.type = + "internal"), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -42,8 +44,9 @@ scale_y_Tfr_internal_continuous( scale_y_Tfr_total_continuous( unit.exponent = ifelse(pc.out, -2, 0), name = Tfr_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols, Tfr.type = "total"), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols, Tfr.type = + "total"), labels = SI_pl_format(exponent = unit.exponent), limits = c(0, 1), format = getOption("photobiology.math", default = "R.expression"), @@ -124,6 +127,11 @@ ggplot(yellow_gel.spct) + scale_y_Tfr_total_continuous(axis.symbols = FALSE) + scale_x_wl_continuous(axis.symbols = FALSE) +ggplot(normalize(yellow_gel.spct)) + + geom_line() + + scale_y_Tfr_total_continuous(normalized = "max") + + scale_x_wl_continuous() + unset_filter_qty_default() } diff --git a/man/scale_y_counts_continuous.Rd b/man/scale_y_counts_continuous.Rd index 720c2cea..e4858beb 100644 --- a/man/scale_y_counts_continuous.Rd +++ b/man/scale_y_counts_continuous.Rd @@ -8,8 +8,8 @@ scale_y_counts_continuous( unit.exponent = ifelse(normalized, 0, 3), name = counts_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["counts"]], @@ -22,7 +22,8 @@ scale_y_counts_continuous( scale_y_counts_tg_continuous( unit.exponent = ifelse(normalized, 0, 3), name = counts_label(unit.exponent = 0, format = format, label.text = label.text, scaled - = scaled, normalized = round(normalized, 1), axis.symbols = axis.symbols), + = scaled, normalized = ifelse(is.numeric(normalized), round(normalized, 1), + unique(normalized)), axis.symbols = axis.symbols), labels = SI_tg_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["counts"]], @@ -84,16 +85,11 @@ ggplot(white_led.raw_spct) + scale_y_counts_tg_continuous(unit.exponent = 0) + scale_x_wl_continuous() -norm_led.raw_spct <- normalize(white_led.raw_spct[ , 1:2], norm = "max") +norm_led.raw_spct <- normalize(white_led.raw_spct, norm = "max") ggplot(norm_led.raw_spct) + geom_line() + - scale_y_counts_continuous(normalized = getNormalized(norm_led.raw_spct)) + - scale_x_wl_continuous() - -ggplot(norm_led.raw_spct) + - geom_line() + - scale_y_counts_tg_continuous(normalized = getNormalized(norm_led.raw_spct)) + + scale_y_counts_continuous(unit.exponent = 0, normalized = "max") + scale_x_wl_continuous() } diff --git a/man/scale_y_cps_continuous.Rd b/man/scale_y_cps_continuous.Rd index 8af69606..dd6298ff 100644 --- a/man/scale_y_cps_continuous.Rd +++ b/man/scale_y_cps_continuous.Rd @@ -7,8 +7,8 @@ scale_y_cps_continuous( unit.exponent = 0, name = cps_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["cps"]], @@ -66,9 +66,20 @@ ggplot(white_led.cps_spct * 1e-4) + norm_led.cps_spct <- normalize(white_led.cps_spct, norm = "max") +ggplot(norm_led.cps_spct) + + geom_line() + + scale_y_cps_continuous(normalized = is_normalized(norm_led.cps_spct)) + + scale_x_wl_continuous() + ggplot(norm_led.cps_spct) + geom_line() + scale_y_cps_continuous(normalized = getNormalized(norm_led.cps_spct)) + scale_x_wl_continuous() +ggplot(norm_led.cps_spct) + + geom_line() + + scale_y_cps_continuous(normalized = + normalization(norm_led.cps_spct)$norm.type) + + scale_x_wl_continuous() + } diff --git a/man/scale_y_multipliers_continuous.Rd b/man/scale_y_multipliers_continuous.Rd index 015fcc46..665b5dbc 100644 --- a/man/scale_y_multipliers_continuous.Rd +++ b/man/scale_y_multipliers_continuous.Rd @@ -7,8 +7,8 @@ scale_y_multipliers_continuous( unit.exponent = 0, name = multipliers_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["e.mult"]], diff --git a/man/scale_y_s.e.irrad_continuous.Rd b/man/scale_y_s.e.irrad_continuous.Rd index e9a1520b..23f2787d 100644 --- a/man/scale_y_s.e.irrad_continuous.Rd +++ b/man/scale_y_s.e.irrad_continuous.Rd @@ -10,8 +10,8 @@ scale_y_s.e.irrad_continuous( unit.exponent = 0, name = s.e.irrad_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.e.irrad"]], @@ -24,8 +24,8 @@ scale_y_s.e.irrad_continuous( scale_y_s.q.irrad_continuous( unit.exponent = ifelse(normalized, 0, -6), name = s.q.irrad_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.q.irrad"]], @@ -38,8 +38,8 @@ scale_y_s.q.irrad_continuous( scale_y_s.e.irrad_log10( unit.exponent = 0, name = s.e.irrad_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.e.irrad"]], @@ -52,8 +52,8 @@ scale_y_s.e.irrad_log10( scale_y_s.q.irrad_log10( unit.exponent = ifelse(normalized, 0, -6), name = s.q.irrad_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.q.irrad"]], @@ -131,11 +131,17 @@ ggplot(clip_wl(sun.spct, c(295, NA)), scale_x_wl_continuous() photon_as_default() -normalized_sun.spct <- normalize(sun.spct) +normalized_sun.spct <- normalize(e2q(sun.spct, action = "replace")) ggplot(normalized_sun.spct) + geom_line(na.rm = TRUE) + scale_y_s.q.irrad_continuous(normalized = - getNormalized(normalized_sun.spct)) + + normalization(normalized_sun.spct)$norm.wl) + + scale_x_wl_continuous() + +ggplot(normalized_sun.spct) + + geom_line(na.rm = TRUE) + + scale_y_s.q.irrad_continuous(normalized = + normalization(normalized_sun.spct)$norm.type) + scale_x_wl_continuous() unset_radiation_unit_default() diff --git a/man/scale_y_s.e.response_continuous.Rd b/man/scale_y_s.e.response_continuous.Rd index caed6a58..1cb7dec7 100644 --- a/man/scale_y_s.e.response_continuous.Rd +++ b/man/scale_y_s.e.response_continuous.Rd @@ -10,8 +10,8 @@ scale_y_s.e.response_continuous( unit.exponent = 0, name = s.e.response_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.e.response"]], @@ -24,8 +24,8 @@ scale_y_s.e.response_continuous( scale_y_s.q.response_continuous( unit.exponent = 0, name = s.q.response_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.q.response"]], @@ -38,8 +38,8 @@ scale_y_s.q.response_continuous( scale_y_s.e.action_continuous( unit.exponent = 0, name = s.e.action_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.e.action"]], @@ -52,8 +52,8 @@ scale_y_s.e.action_continuous( scale_y_s.q.action_continuous( unit.exponent = 0, name = s.q.action_label(unit.exponent = unit.exponent, format = format, label.text = - label.text, scaled = scaled, normalized = round(normalized, 1), axis.symbols = - axis.symbols), + label.text, scaled = scaled, normalized = ifelse(is.numeric(normalized), + round(normalized, 1), unique(normalized)), axis.symbols = axis.symbols), labels = SI_pl_format(exponent = -unit.exponent), format = getOption("photobiology.math", default = "R.expression"), label.text = axis_labels()[["s.q.action"]], @@ -125,6 +125,12 @@ ggplot(norm_ccd.spct) + scale_y_s.e.response_continuous(normalized = getNormalized(norm_ccd.spct)) + scale_x_wl_continuous() +ggplot(norm_ccd.spct) + + geom_line() + + scale_y_s.e.response_continuous(normalized = + normalization(norm_ccd.spct)$norm.type) + + scale_x_wl_continuous() + photon_as_default() norm_ccd.spct <- normalize(ccd.spct, norm = "max") diff --git a/man/validate_idfactor.Rd b/man/validate_idfactor.Rd deleted file mode 100644 index dd9c6fba..00000000 --- a/man/validate_idfactor.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/autoplot-utils.R -\name{validate_idfactor} -\alias{validate_idfactor} -\title{Validate idfactor} -\usage{ -validate_idfactor(idfactor) -} -\arguments{ -\item{idfactor}{character, logical, NULL or NA. If a \code{character} string, -it is validated as an R name, while logical values, NULL and NA are -returned unchanged.} -} -\description{ -Validate idfactor -} -\keyword{internal} diff --git a/man/warn_norm_arg.Rd b/man/warn_norm_arg.Rd new file mode 100644 index 00000000..2c921910 --- /dev/null +++ b/man/warn_norm_arg.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils-internal.R +\name{warn_norm_arg} +\alias{warn_norm_arg} +\title{Warn if norm argument passed in call} +\usage{ +warn_norm_arg(norm) +} +\arguments{ +\item{norm}{numeric or character No longer supported, normalization is always +updated in \code{autoplot()} if present and a unit conversion applied.} +} +\description{ +Warn if norm argument passed in call +} +\keyword{internal} diff --git a/tests/testthat/_snaps/plot-methods/cps-default.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-default.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-default.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-default.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-minus-annotations.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-minus-annotations.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-minus-annotations.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-minus-annotations.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-no-annotations.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-no-annotations.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-no-annotations.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-no-annotations.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-plus-annotations.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-plus-annotations.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-plus-annotations.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-plus-annotations.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-range-num.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-range-num.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-range-num.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-range-num.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-range-wb.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-range-wb.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-range-wb.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-range-wb.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-reserve-space.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-reserve-space.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-reserve-space.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-reserve-space.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-ylim1.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-ylim1.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-ylim1.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-ylim1.svg diff --git a/tests/testthat/_snaps/plot-methods/cps-ylim2.svg b/tests/testthat/_snaps/autoplot-cps-spct/cps-ylim2.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/cps-ylim2.svg rename to tests/testthat/_snaps/autoplot-cps-spct/cps-ylim2.svg diff --git a/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-normalized.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-normalized.svg new file mode 100644 index 00000000..9fad2a2a --- /dev/null +++ b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-normalized.svg @@ -0,0 +1,215 @@ + + + + + + + + + + + + + + + + + + + + + + +300 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVB +0.06 +UVA +0.29 +PhR +0.62 +C +o +n +t +r +i +b +u +t +i +o +n + + +t +o + + +t +o +t +a +l +A + + +( +/1 +) + + + +0.0 +0.2 +0.4 +0.6 + + + + + + + + + + +300 +400 +500 +600 +700 +800 +Wavelength, +Îğ + +( +n +m +) +Internal + + +s +p +e +c +t +r +a +l + + +a +b +s +o +r +b +a +n +c +e + + +A +Îğ +int + +A +Îğ += +250 +int + + +( +rel. +) +filter-default-a-normalized + + diff --git a/tests/testthat/_snaps/plot-methods/filter-default-a-scaled.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-scaled.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-a-scaled.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-scaled.svg diff --git a/tests/testthat/_snaps/plot-methods/filter-default-a-ylim.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-ylim.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-a-ylim.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-a-ylim.svg diff --git a/tests/testthat/_snaps/plot-methods/filter-default-a.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-a.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-a.svg diff --git a/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a2t.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a2t.svg new file mode 100644 index 00000000..b8c49722 --- /dev/null +++ b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-a2t.svg @@ -0,0 +1,192 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVB +0.00204 +UVA +0.00753 +PhR +0.0703 +T +Îğ +i +n +t + +( +/1 +) + + + +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +Wavelength, +Îğ + +( +n +m +) +Internal + + +s +p +e +c +t +r +a +l + + +t +r +a +n +s +m +i +t +t +a +n +c +e + + +T +Îğ +int + + +( +/1 +) +filter-default-a2t + + diff --git a/tests/testthat/_snaps/plot-methods/filter-default-apt-ylim.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt-ylim.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-apt-ylim.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt-ylim.svg diff --git a/tests/testthat/_snaps/plot-methods/filter-default-apt.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-apt.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt.svg diff --git a/tests/testthat/_snaps/plot-methods/filter-mspct-mean-a.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2a.svg similarity index 91% rename from tests/testthat/_snaps/plot-methods/filter-mspct-mean-a.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2a.svg index a96baf58..a2284062 100644 --- a/tests/testthat/_snaps/plot-methods/filter-mspct-mean-a.svg +++ b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2a.svg @@ -27,7 +27,7 @@ - + @@ -100,13 +100,13 @@ ]UVC -5 +4.85 UVB -3 +2.85 UVA -2.34 +2.19 PhR -1.48 +1.33 A Îğ i @@ -121,13 +121,13 @@ 0 -2 -4 -6 +2 +4 +6 - - - + + + @@ -181,6 +181,6 @@ A U ) -filter-mspct-mean-A +filter-default-apt2a diff --git a/tests/testthat/_snaps/plot-methods/filter-default-norm-max.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2t.svg similarity index 73% rename from tests/testthat/_snaps/plot-methods/filter-default-norm-max.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2t.svg index 5e8df3e8..f1188a3f 100644 --- a/tests/testthat/_snaps/plot-methods/filter-default-norm-max.svg +++ b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-apt2t.svg @@ -27,7 +27,7 @@ - + @@ -100,42 +100,22 @@ ]UVC -0.00 +4.91e-05 UVB -0.00 +0.00156 UVA -0.00 +0.00753 PhR -0.14 -C -o -n -t -r -i -b -u -t -i -o -n - - -t -o - - -t -o -t -a -l -T - - -( -/1 -) +0.0703 +T +Îğ +i +n +t + +( +/1 +) @@ -168,48 +148,42 @@ n m ) -Internal - - -s -p -e -c -t -r -a -l - - -t -r -a -n -s -m -i -t -t -a -n -c -e - - -T -Îğ -int - -T -Îğ -= -765.2 -int - - -( -rel. -) -filter-default-norm-max +Internal + + +s +p +e +c +t +r +a +l + + +t +r +a +n +s +m +i +t +t +a +n +c +e + + +T +Îğ +int + + +( +/1 +) +filter-default-apt2t diff --git a/tests/testthat/_snaps/plot-methods/filter-default-normalized.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-default-normalized.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-default-normalized.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-default-normalized.svg diff --git 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-450 -500 -550 -600 -650 -700 -750 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -a -b -s -o -r -p -t -a -n -c -e - - -A -Îğ - - -( -/1 -) +0.00 +0.25 +0.50 +0.75 +1.00 + + + + + + + + + + + + + +400 +450 +500 +550 +600 +650 +700 +750 +Wavelength, +Îğ + +( +n +m +) +Internal + + +s +p +e +c +t +r +a +l + + +t +r +a +n +s +m +i +t +t +a +n +c +e + + +T +Îğ +int + + +( +/1 +) spct.idx @@ -237,6 +243,6 @@ one half -filter-mspct-default-Afr +filter-mspct-default-Afr diff --git a/tests/testthat/_snaps/plot-methods/filter-mspct-default-range.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-mspct-default-range.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/filter-mspct-default-range.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-mspct-default-range.svg diff --git a/tests/testthat/_snaps/plot-methods/filter-mspct-default-tfr.svg b/tests/testthat/_snaps/autoplot-filter-spct/filter-mspct-default-tfr.svg similarity index 61% rename from tests/testthat/_snaps/plot-methods/filter-mspct-default-tfr.svg rename to tests/testthat/_snaps/autoplot-filter-spct/filter-mspct-default-tfr.svg index a80addb2..b2ecb4a4 100644 --- a/tests/testthat/_snaps/plot-methods/filter-mspct-default-tfr.svg +++ b/tests/testthat/_snaps/autoplot-filter-spct/filter-mspct-default-tfr.svg @@ -33,101 +33,137 @@ - - - + + + + - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]UVC -UVB -UVA -PhR + + + + + + + + + + +750 +750 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +PhR 0.00 @@ -140,18 +176,22 @@ - - - - - - -300 -400 -500 -600 -700 -800 + + + + + + + + +400 +450 +500 +550 +600 +650 +700 +750 Wavelength, Îğ diff --git 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b/tests/testthat/_snaps/autoplot-response-spct/response-minus-annotations.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/response-minus-annotations.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-minus-annotations.svg diff --git a/tests/testthat/_snaps/plot-methods/response-minus-boxes-q.svg b/tests/testthat/_snaps/autoplot-response-spct/response-minus-boxes-q.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/response-minus-boxes-q.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-minus-boxes-q.svg diff --git a/tests/testthat/_snaps/plot-methods/response-minus-summaries-q.svg b/tests/testthat/_snaps/autoplot-response-spct/response-minus-summaries-q.svg similarity index 100% rename from tests/testthat/_snaps/plot-methods/response-minus-summaries-q.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-minus-summaries-q.svg diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-default-e.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-e.svg similarity index 87% rename from tests/testthat/_snaps/plot-methods/response-mspct-default-e.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-e.svg index e2e57a3f..a916d8a1 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-default-e.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-e.svg @@ -128,63 +128,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) spct.idx diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-default-p.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-p.svg similarity index 87% rename from tests/testthat/_snaps/plot-methods/response-mspct-default-p.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-p.svg index 5f338814..23b1531f 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-default-p.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-p.svg @@ -139,63 +139,63 @@ n m ) -S -p -e -c -t -r -a -l - - -p -h -o -t -o -n - - -r -e -s -p -o -n -s -e - - -R -Q - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +p +h +o +t +o +n + + +r +e +s +p +o +n +s +e + + +R +Q + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) spct.idx diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-default-range.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-range.svg similarity index 88% rename from tests/testthat/_snaps/plot-methods/response-mspct-default-range.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-range.svg index 1d63f410..ac05eb76 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-default-range.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default-range.svg @@ -166,63 +166,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) spct.idx diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-default.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default.svg similarity index 87% rename from tests/testthat/_snaps/plot-methods/response-mspct-default.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-default.svg index 7d021a0e..00639ea3 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-default.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-default.svg @@ -128,63 +128,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) spct.idx diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-mean-e.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-e.svg similarity index 86% rename from tests/testthat/_snaps/plot-methods/response-mspct-mean-e.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-e.svg index 1f7f02a8..64ef7fc7 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-mean-e.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-e.svg @@ -125,63 +125,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-mean-e diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-mean-p.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-p.svg similarity index 85% rename from tests/testthat/_snaps/plot-methods/response-mspct-mean-p.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-p.svg index 97935aaf..ad9cff8a 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-mean-p.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean-p.svg @@ -123,63 +123,63 @@ n m ) -S -p -e -c -t -r -a -l - - -p -h -o -t -o -n - - -r -e -s -p -o -n -s -e - - -R -Q - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +p +h +o +t +o +n + + +r +e +s +p +o +n +s +e + + +R +Q + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-mean-p diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-mean.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean.svg similarity index 86% rename from tests/testthat/_snaps/plot-methods/response-mspct-mean.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean.svg index 394be119..35860218 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-mean.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-mean.svg @@ -125,63 +125,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-mean diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-median-e.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-e.svg similarity index 86% rename from tests/testthat/_snaps/plot-methods/response-mspct-median-e.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-e.svg index b9e0ddde..8d522cc0 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-median-e.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-e.svg @@ -125,63 +125,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-median-e diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-median-p.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-p.svg similarity index 85% rename from tests/testthat/_snaps/plot-methods/response-mspct-median-p.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-p.svg index 50e5b8db..9dde873b 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-median-p.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median-p.svg @@ -123,63 +123,63 @@ n m ) -S -p -e -c -t -r -a -l - - -p -h -o -t -o -n - - -r -e -s -p -o -n -s -e - - -R -Q - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +p +h +o +t +o +n + + +r +e +s +p +o +n +s +e + + +R +Q + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-median-p diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-median.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median.svg similarity index 86% rename from tests/testthat/_snaps/plot-methods/response-mspct-median.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-median.svg index 8632b33f..309a3720 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-median.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-median.svg @@ -125,63 +125,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) response-mspct-median diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-no-annotations.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-no-annotations.svg similarity index 82% rename from tests/testthat/_snaps/plot-methods/response-mspct-no-annotations.svg rename to tests/testthat/_snaps/autoplot-response-spct/response-mspct-no-annotations.svg index 31fdc884..c34299c6 100644 --- a/tests/testthat/_snaps/plot-methods/response-mspct-no-annotations.svg +++ b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-no-annotations.svg @@ -78,63 +78,63 @@ n m ) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - - -( -r -e -s -p -. - - -u -n -i -t - - -d -− -1 - -n -m -− -1 -) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +r +e +s +p +o +n +s +e + + +R +E + +Îğ + + +( +r +e +s +p +. + + +u +n +i +t + + +s +− +1 + +n +m +− +1 +) spct.idx diff --git a/tests/testthat/_snaps/plot-methods/response-mspct-reserve-space.svg b/tests/testthat/_snaps/autoplot-response-spct/response-mspct-reserve-space.svg similarity index 81% 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a/tests/testthat/_snaps/plot-methods/source-mspct-default-e.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-e.svg similarity index 50% rename from tests/testthat/_snaps/plot-methods/source-mspct-default-e.svg rename to tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-e.svg index 2de7741e..590c63e6 100644 --- a/tests/testthat/_snaps/plot-methods/source-mspct-default-e.svg +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-e.svg @@ -21,193 +21,190 @@ - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - -604.4 -604.4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]UVC -UVB -UVA -PhR + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVC +UVB +UVA +PhR -0e+00 -2e-07 -4e-07 -6e-07 -8e-07 - - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -900 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -e -x -p -o -s -u -r -e - - -E -Îğ - - -( -M -J - -d -− -1 - -m -− -2 - -n -m -− -1 -) +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) spct.idx @@ -216,6 +213,6 @@ one half -source-mspct-default-e +source-mspct-default-e diff --git a/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-geom-spct.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-geom-spct.svg new file mode 100644 index 00000000..79f49c15 --- /dev/null +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-geom-spct.svg @@ -0,0 +1,226 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVC +UVB +UVA +PhR + + +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) + +spct.idx + + + + + + +one +half +source-mspct-default-geom-spct + + diff --git a/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-idfactor.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-idfactor.svg new file mode 100644 index 00000000..0f892695 --- /dev/null +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-idfactor.svg @@ -0,0 +1,218 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVC +UVB +UVA +PhR + + +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) + +spectrum + + + + +one +half +source-mspct-default-idfactor + + diff --git a/tests/testthat/_snaps/plot-methods/source-mspct-default-p.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-p.svg similarity index 50% rename from tests/testthat/_snaps/plot-methods/source-mspct-default-p.svg rename to tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-p.svg index 95a8e11d..e687eaac 100644 --- a/tests/testthat/_snaps/plot-methods/source-mspct-default-p.svg +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-p.svg @@ -18,197 +18,200 @@ - + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - -611 -611 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]UVC -UVB -UVA -PAR + + + + + + + + + + + + + + + + + + + + + + + + + + + +611 +611 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVC +UVB +UVA +PAR -0e+00 -1e-06 -2e-06 -3e-06 -4e-06 - - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -900 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -p -h -o -t -o -n - - -e -x -p -o -s -u -r -e - - -Q -Îğ - - -( -m -o -l - -d -− -1 - -m -− -2 - -n -m -− -1 -) +0 +1 +2 +3 +4 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +p +h +o +t +o +n + + +i +r +r +a +d +i +a +n +c +e + + +Q +Îğ + + +( +Îĵ +m +o +l + +s +− +1 + +m +− +2 + +n +m +− +1 +) spct.idx @@ -217,6 +220,6 @@ one half -source-mspct-default-p +source-mspct-default-p diff --git a/tests/testthat/_snaps/plot-methods/source-mspct-default-range.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-range.svg similarity index 54% rename from tests/testthat/_snaps/plot-methods/source-mspct-default-range.svg rename to tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-range.svg index 85e07a25..99195485 100644 --- a/tests/testthat/_snaps/plot-methods/source-mspct-default-range.svg +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-range.svg @@ -21,207 +21,204 @@ - - + + - - - - - - - - - - - - - - - - - - - - - - -604.4 -604.4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]PhR[ + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]PhR[ -0e+00 -2e-07 -4e-07 -6e-07 -8e-07 - - - - - - - - - - -500 -550 -600 -650 -700 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -e -x -p -o -s -u -r -e - - -E -Îğ - - -( -M -J - -d -− -1 - -m -− -2 - -n -m -− -1 -) +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + +500 +550 +600 +650 +700 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) spct.idx @@ -230,6 +227,6 @@ one half -source-mspct-default-range +source-mspct-default-range diff --git a/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-null.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-null.svg new file mode 100644 index 00000000..5c9e98e0 --- /dev/null +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-null.svg @@ -0,0 +1,212 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Total + + +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) + +spct.idx + + + + +one +half +source-mspct-default-wband-null + + diff --git a/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-wb.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-wb.svg new file mode 100644 index 00000000..993dce85 --- /dev/null +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default-wband-wb.svg @@ -0,0 +1,212 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + 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+Yellow +Orange +Red + + +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) + +spct.idx + + + + +one +half +source-mspct-default-wband-wbls + + diff --git a/tests/testthat/_snaps/plot-methods/source-mspct-default.svg b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default.svg similarity index 50% rename from tests/testthat/_snaps/plot-methods/source-mspct-default.svg rename to tests/testthat/_snaps/autoplot-source-spct/source-mspct-default.svg index 597ce74d..d2556849 100644 --- a/tests/testthat/_snaps/plot-methods/source-mspct-default.svg +++ b/tests/testthat/_snaps/autoplot-source-spct/source-mspct-default.svg @@ -21,193 +21,190 @@ - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - -604.4 -604.4 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -]UVC -UVB -UVA -PhR + + + + + + + + + + + + + + + + + + + + + + + + + + + +604.4 +604.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]UVC +UVB +UVA +PhR -0e+00 -2e-07 -4e-07 -6e-07 -8e-07 - - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -900 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -e -x -p -o -s -u -r -e - - -E -Îğ - - -( -M -J - -d -− -1 - -m -− -2 - -n -m -− -1 -) +0.0 +0.2 +0.4 +0.6 +0.8 + + + + + + + + + + + + +300 +400 +500 +600 +700 +800 +900 +Wavelength, +Îğ + +( +n +m +) +S +p +e +c +t +r +a +l + + +e +n +e +r +g +y + + +i +r +r +a +d +i +a +n +c +e + + +E +Îğ + + +( +W + +m +− +2 + +n +m +− +1 +) spct.idx @@ -216,6 +213,6 @@ one half -source-mspct-default +source-mspct-default diff --git a/tests/testthat/_snaps/autoplot-source-spct/source-mspct-facets1.svg 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a/tests/testthat/_snaps/plot-methods/waveband-plus-segments.svg b/tests/testthat/_snaps/plot-methods/waveband-plus-segments.svg deleted file mode 100644 index b7322708..00000000 --- a/tests/testthat/_snaps/plot-methods/waveband-plus-segments.svg +++ /dev/null @@ -1,187 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Red - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - -R -E - -Îğ -= -610 - - -( -rel. -) -waveband-plus-segments - - diff --git a/tests/testthat/_snaps/plot-methods/waveband-reserve-space.svg b/tests/testthat/_snaps/plot-methods/waveband-reserve-space.svg deleted file mode 100644 index 84c7b042..00000000 --- a/tests/testthat/_snaps/plot-methods/waveband-reserve-space.svg +++ /dev/null @@ -1,109 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - -R -E - -Îğ -= -610 - - -( -rel. -) -waveband-reserve-space - - diff --git a/tests/testthat/_snaps/plot-methods/waveband-text-size.svg b/tests/testthat/_snaps/plot-methods/waveband-text-size.svg deleted file mode 100644 index cb933186..00000000 --- a/tests/testthat/_snaps/plot-methods/waveband-text-size.svg +++ /dev/null @@ -1,187 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Red - - - -0.00 -0.25 -0.50 -0.75 -1.00 - - - - - - - - - - - -300 -400 -500 -600 -700 -800 -Wavelength, -Îğ - -( -n -m -) -S -p -e -c -t -r -a -l - - -e -n -e -r -g -y - - -r -e -s -p -o -n -s -e - - -R -E - -Îğ - -R -E - -Îğ -= -610 - - -( -rel. -) -waveband-text-size - - diff --git a/tests/testthat/test-autoplot-cps-spct.R b/tests/testthat/test-autoplot-cps-spct.R new file mode 100644 index 00000000..9dbd3c01 --- /dev/null +++ b/tests/testthat/test-autoplot-cps-spct.R @@ -0,0 +1,33 @@ +context("autoplot-cps") +library(ggplot2) +library(photobiology) + +# We prepare shorter data objects for spectra to improve tests' runtime. +# We also make sure no data are exactly at the boundary of the possible range to +# avoid warnings. Such values are physically possible but not measurable. +length.out.spct <- 100L +white_led.cps_spct <- interpolate_spct(photobiology::white_led.cps_spct, + length.out = length.out.spct) + +test_that("cps_spct", { + set_annotations_default() + vdiffr::expect_doppelganger("cps-default", + autoplot(white_led.cps_spct)) + vdiffr::expect_doppelganger("cps-ylim1", + autoplot(white_led.cps_spct, ylim = c(NA, 5e5))) + vdiffr::expect_doppelganger("cps-ylim2", + autoplot(white_led.cps_spct, ylim = c(-1e5, 5e5))) + vdiffr::expect_doppelganger("cps-range-num", + autoplot(white_led.cps_spct, range = c(500, 700))) + vdiffr::expect_doppelganger("cps-range-wb", + autoplot(white_led.cps_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("cps-no-annotations", + autoplot(white_led.cps_spct, annotations = "")) + vdiffr::expect_doppelganger("cps-reserve-space", + autoplot(white_led.cps_spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("cps-minus-annotations", + autoplot(white_led.cps_spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("cps-plus-annotations", + autoplot(white_led.cps_spct, annotations = c("+", "boundaries"))) +}) + diff --git a/tests/testthat/test-autoplot-filter-spct.R b/tests/testthat/test-autoplot-filter-spct.R new file mode 100644 index 00000000..6bac3614 --- /dev/null +++ b/tests/testthat/test-autoplot-filter-spct.R @@ -0,0 +1,414 @@ +context("autoplot-filter") +library(ggplot2) +library(photobiology) +library(photobiologyWavebands) + +# We prepare shorter data objects for spectra to improve tests' runtime. +# We also make sure no data are exactly at the boundary of the possible range to +# avoid warnings. Such values are physically possible but not measurable. +length.out.spct <- 100L +Ler_leaf_trns.spct <- interpolate_spct(photobiology::Ler_leaf_trns.spct, length.out = length.out.spct) +Ler_leaf_trns.spct <- clean(Ler_leaf_trns.spct, range.s.data = c(1e-5, 1 - 1e-5)) +Ler_leaf_trns_i.spct <- interpolate_spct(photobiology::Ler_leaf_trns_i.spct, length.out = length.out.spct) +Ler_leaf_trns_i.spct <- clean(Ler_leaf_trns_i.spct, range.s.data = c(1e-5, 1 - 1e-5)) +Ler_leaf_rflt.spct <- interpolate_spct(photobiology::Ler_leaf_rflt.spct, length.out = length.out.spct) +Ler_leaf_rflt.spct <- clean(Ler_leaf_rflt.spct, range.s.data = c(1e-5, 1 - 1e-5)) +Ler_leaf.spct <- clean(Ler_leaf.spct, min.Afr = 1e-5, range.s.data = c(1e-5, 1 - 1e-5)) +Ler_leaf.spct <- interpolate_spct(photobiology::Ler_leaf.spct, length.out = length.out.spct) +Ler_leaf.spct <- clean(Ler_leaf.spct, min.Afr = 1e-5, range.s.data = c(1e-5, 1 - 1e-5)) + + +test_that("filter_spct default", { + set_annotations_default() + Tfr_as_default() + + vdiffr::expect_doppelganger("filter-default-tot-scaled", + autoplot(fscale(Ler_leaf_trns.spct, target = 0.06, + range = c(400,700), set.scaled = TRUE))) + vdiffr::expect_doppelganger("filter-default-tot-normalized", + autoplot(normalize(Ler_leaf_trns.spct, norm = "max"))) + + vdiffr::expect_doppelganger("filter-default-tot", + autoplot(Ler_leaf_trns.spct)) + vdiffr::expect_doppelganger("filter-default-tot2a", + autoplot(Ler_leaf_trns.spct, plot.qty = "absorbance")) + # vdiffr::expect_doppelganger("filter-default-tot2afr", + # autoplot(Ler_leaf_trns.spct, plot.qty = "absorptance")) + vdiffr::expect_doppelganger("filter-default-tot-ylim", + autoplot(Ler_leaf_trns.spct, ylim = c(-0.05, 0.5))) + vdiffr::expect_doppelganger("filter-default-pc-out-tot", + autoplot(Ler_leaf_trns.spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("filter-text-size-tot", + autoplot(Ler_leaf_trns.spct, text.size = 3.5)) + vdiffr::expect_doppelganger("filter-span-31-tot", + autoplot(Ler_leaf_trns.spct, span = 31)) + vdiffr::expect_doppelganger("filter-wb-vis-tot", + autoplot(Ler_leaf_trns.spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("filter-label-average-tot", + autoplot(Ler_leaf_trns.spct, label.qty = "average")) + vdiffr::expect_doppelganger("filter-label-mean-tot", + autoplot(Ler_leaf_trns.spct, label.qty = "mean")) + vdiffr::expect_doppelganger("filter-range-num-tot", + autoplot(Ler_leaf_trns.spct, range = c(500, 700))) + vdiffr::expect_doppelganger("filter-range-wb-tot", + autoplot(Ler_leaf_trns.spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("filter-no-annotations-tot", + autoplot(Ler_leaf_trns.spct, annotations = "")) + vdiffr::expect_doppelganger("filter-minus-annotations-tot", + autoplot(Ler_leaf_trns.spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("filter-plus-annotations-tot", + autoplot(Ler_leaf_trns.spct, annotations = c("+", "boundaries"))) + + vdiffr::expect_doppelganger("filter-default-scaled", + autoplot(fscale(Ler_leaf_trns_i.spct, target = 0.06, + range = c(400,700), set.scaled = TRUE))) + vdiffr::expect_doppelganger("filter-default-normalized", + autoplot(normalize(Ler_leaf_trns_i.spct, norm = "max"))) + + vdiffr::expect_doppelganger("filter-default", + autoplot(Ler_leaf_trns_i.spct)) + vdiffr::expect_doppelganger("filter-default-ylim", + autoplot(Ler_leaf_trns_i.spct, ylim = c(NA, 1.2))) + vdiffr::expect_doppelganger("filter-default-pc-out", + autoplot(Ler_leaf_trns_i.spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("filter-text-size", + autoplot(Ler_leaf_trns_i.spct, text.size = 3.5)) + vdiffr::expect_doppelganger("filter-span-31", + autoplot(Ler_leaf_trns_i.spct, span = 31)) + vdiffr::expect_doppelganger("filter-wb-vis", + autoplot(Ler_leaf_trns_i.spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("filter-label-average", + autoplot(Ler_leaf_trns_i.spct, label.qty = "average")) + vdiffr::expect_doppelganger("filter-label-mean", + autoplot(Ler_leaf_trns_i.spct, label.qty = "mean")) + vdiffr::expect_doppelganger("filter-range-num", + autoplot(Ler_leaf_trns_i.spct, range = c(500, 700))) + vdiffr::expect_doppelganger("filter-range-wb", + autoplot(Ler_leaf_trns_i.spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("filter-no-annotations", + autoplot(Ler_leaf_trns_i.spct, annotations = "")) + vdiffr::expect_doppelganger("filter-reserve-space", + autoplot(Ler_leaf_trns_i.spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("filter-minus-summaries", + autoplot(Ler_leaf_trns_i.spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("filter-minus-boxes", + autoplot(Ler_leaf_trns_i.spct, annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("filter-plus-boundaries", + autoplot(Ler_leaf_trns_i.spct, annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("filter-plus-segments", + autoplot(Ler_leaf_trns_i.spct, annotations = c("+", "segments"))) +}) + +test_that("filter_spct absorptance", { + set_annotations_default() + Afr_as_default() + + Ler_leaf_Afr_i_spct <- T2Afr(Ler_leaf_trns_i.spct) + + vdiffr::expect_doppelganger("filter-default-apt", + autoplot(Ler_leaf_Afr_i_spct)) + vdiffr::expect_doppelganger("filter-default-apt2t", + autoplot(Ler_leaf_Afr_i_spct, + plot.qty = "transmittance")) + vdiffr::expect_doppelganger("filter-default-apt2a", + autoplot(Ler_leaf_Afr_i_spct, + plot.qty = "absorbance")) + vdiffr::expect_doppelganger("filter-default-apt-ylim", + autoplot(Ler_leaf_Afr_i_spct, ylim = c(-0.1, 1.2))) + vdiffr::expect_doppelganger("filter-default-pc-out-apt", + autoplot(Ler_leaf_Afr_i_spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("filter-text-size-apt", + autoplot(Ler_leaf_Afr_i_spct, text.size = 3.5)) + vdiffr::expect_doppelganger("filter-span-31-apt", + autoplot(Ler_leaf_Afr_i_spct, span = 31)) + vdiffr::expect_doppelganger("filter-wb-vis-apt", + autoplot(Ler_leaf_Afr_i_spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("filter-label-average-apt", + autoplot(Ler_leaf_Afr_i_spct, label.qty = "average")) + vdiffr::expect_doppelganger("filter-label-mean-apt", + autoplot(Ler_leaf_Afr_i_spct, label.qty = "mean")) + vdiffr::expect_doppelganger("filter-range-num-apt", + autoplot(Ler_leaf_Afr_i_spct, range = c(500, 700))) + vdiffr::expect_doppelganger("filter-range-wb-apt", + autoplot(Ler_leaf_Afr_i_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("filter-no-annotations-apt", + autoplot(Ler_leaf_Afr_i_spct, annotations = "")) + vdiffr::expect_doppelganger("filter-minus-summaries-q", + autoplot(Ler_leaf_Afr_i_spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("filter-minus-boxes-apt", + autoplot(Ler_leaf_Afr_i_spct, annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("filter-plus-boundaries-apt", + autoplot(Ler_leaf_Afr_i_spct, annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("filter-plus-segments-apt", + autoplot(Ler_leaf_Afr_i_spct, annotations = c("+", "segments"))) +}) + +test_that("filter_spct A", { + set_annotations_default() + A_as_default() + + Ler_leaf_A_i_spct <- T2A(Ler_leaf_trns_i.spct, action = "replace") + + vdiffr::expect_doppelganger("filter-default-a2t", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), + plot.qty = "transmittance")) + # vdiffr::expect_doppelganger("filter-default-a2afr", + # autoplot(Ler_leaf_A_i_spct, range = c(300, NA), + # plot.qty = "absorptance")) + vdiffr::expect_doppelganger("filter-default-a-scaled", + autoplot(fscale(Ler_leaf_A_i_spct, target = 2, + range = c(400,700), set.scaled = TRUE), + plot.qty = "absorbance", range = c(300, NA))) + vdiffr::expect_doppelganger("filter-default-a-normalized", + autoplot(normalize(Ler_leaf_A_i_spct, norm = "max"), + range = c(300, NA))) + + vdiffr::expect_doppelganger("filter-default-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA))) + vdiffr::expect_doppelganger("filter-default-a-ylim", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), ylim = c(-0.2, 4))) + vdiffr::expect_doppelganger("filter-text-size-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), text.size = 3.5)) + vdiffr::expect_doppelganger("filter-span-31-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), span = 11)) + vdiffr::expect_doppelganger("filter-wb-vis-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), w.band = VIS_bands())) + vdiffr::expect_doppelganger("filter-label-average-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), label.qty = "average")) + vdiffr::expect_doppelganger("filter-label-mean-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), label.qty = "mean")) + vdiffr::expect_doppelganger("filter-range-wb-a", + autoplot(Ler_leaf_A_i_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("filter-no-annotations-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), annotations = "")) + vdiffr::expect_doppelganger("filter-minus-summaries-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("filter-minus-boxes-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("filter-plus-boundaries-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("filter-plus-segments-a", + autoplot(Ler_leaf_A_i_spct, range = c(300, NA), annotations = c("+", "segments"))) +}) + +test_that("filter_spct Tfr", { + set_annotations_default() + Tfr_as_default() + + Ler_leaf_t_i_spct <- any2T(Ler_leaf_trns_i.spct, action = "replace") + + vdiffr::expect_doppelganger("filter-default-tfr", + autoplot(Ler_leaf_t_i_spct)) + vdiffr::expect_doppelganger("filter-default-tfr-ylim", + autoplot(Ler_leaf_t_i_spct, ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("filter-default-pc-out-tfr", + autoplot(Ler_leaf_t_i_spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("filter-text-size-tfr", + autoplot(Ler_leaf_t_i_spct, text.size = 3.5)) + vdiffr::expect_doppelganger("filter-span-31-tfr", + autoplot(Ler_leaf_t_i_spct, span = 31)) + vdiffr::expect_doppelganger("filter-wb-vis-tfr", + autoplot(Ler_leaf_t_i_spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("filter-label-average-tfr", + autoplot(Ler_leaf_t_i_spct, label.qty = "average")) + vdiffr::expect_doppelganger("filter-label-mean-tfr", + autoplot(Ler_leaf_t_i_spct, label.qty = "mean")) + vdiffr::expect_doppelganger("filter-range-num-tfr", + autoplot(Ler_leaf_t_i_spct, range = c(500, 700))) + vdiffr::expect_doppelganger("filter-range-wb-tfr", + autoplot(Ler_leaf_t_i_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("filter-no-annotations-tfr", + autoplot(Ler_leaf_t_i_spct, annotations = "")) + vdiffr::expect_doppelganger("filter-minus-summaries-tfr", + autoplot(Ler_leaf_t_i_spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("filter-minus-boxes-tfr", + autoplot(Ler_leaf_t_i_spct, annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("filter-plus-boundaries-tfr", + autoplot(Ler_leaf_t_i_spct, annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("filter-plus-segments-tfr", + autoplot(Ler_leaf_t_i_spct, annotations = c("+", "segments"))) +}) + +test_that("filter_mspct", { + unset_filter_qty_default() + set_annotations_default() + + two_leaves.mspct <- filter_mspct(list(one = Ler_leaf_trns_i.spct, + half = Ler_leaf_trns_i.spct / 2)) + vdiffr::expect_doppelganger("filter-mspct-default", + autoplot(two_leaves.mspct)) + vdiffr::expect_doppelganger("filter-mspct-default-ylim", + autoplot(two_leaves.mspct, ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("filter-mspct-default-range", + autoplot(two_leaves.mspct, range = c(500, 700))) + # use range to avoid Tfr == 0 values. + vdiffr::expect_doppelganger("filter-mspct-default-A", + autoplot(T2A(two_leaves.mspct, action = "replace"), + range = c(400,750))) + vdiffr::expect_doppelganger("filter-mspct-default-Afr", + autoplot(T2Afr(two_leaves.mspct, action = "replace"), + range = c(400,750))) + vdiffr::expect_doppelganger("filter-mspct-default-Tfr", + autoplot(any2T(two_leaves.mspct, action = "replace"), + range = c(400,750))) + vdiffr::expect_doppelganger("filter-mspct-no-annotations", + autoplot(two_leaves.mspct, annotations = "")) + vdiffr::expect_doppelganger("filter-mspct-reserve-space", + autoplot(two_leaves.mspct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("filter-mspct-mean", + autoplot(two_leaves.mspct, plot.data = "mean")) + vdiffr::expect_doppelganger("filter-mspct-median", + autoplot(two_leaves.mspct, plot.data = "median")) + # triggers warning + # vdiffr::expect_doppelganger("filter-mspct-sum", + # autoplot(two_leaves.mspct, plot.data = "sum")) + testthat::expect_warning(autoplot(two_leaves.mspct, plot.data = "sum")) + vdiffr::expect_doppelganger("filter-mspct-sum", + autoplot(two_leaves.mspct, plot.data = "prod")) + vdiffr::expect_doppelganger("filter-mspct-se", + autoplot(two_leaves.mspct, plot.data = "se")) + vdiffr::expect_doppelganger("filter-mspct-se-ylab", + autoplot(two_leaves.mspct, plot.data = "se", ylab = "Standard error of the mean")) + vdiffr::expect_doppelganger("filter-mspct-var", + autoplot(two_leaves.mspct, plot.data = "var")) + vdiffr::expect_doppelganger("filter-mspct-var-ylab", + autoplot(two_leaves.mspct, plot.data = "var", ylab = "Variance")) + vdiffr::expect_doppelganger("filter-mspct-mean-Tfr", + autoplot(any2T(two_leaves.mspct, action = "replace"), plot.data = "mean")) + vdiffr::expect_doppelganger("filter-mspct-median-Tfr", + autoplot(any2T(two_leaves.mspct, action = "replace"), plot.data = "median")) + # Bug in photobiology::rowwise_filter() (fixed in photobiology >= 0.10.11) affected next two staements + vdiffr::expect_doppelganger("filter-mspct-mean-Afr", + autoplot(T2Afr(two_leaves.mspct, action = "replace"), plot.data = "mean")) + vdiffr::expect_doppelganger("filter-mspct-median-Afr", + autoplot(T2Afr(two_leaves.mspct, action = "replace"), plot.data = "median")) + vdiffr::expect_doppelganger("filter-mspct-mean-A", + autoplot(T2A(two_leaves.mspct, action = "replace"), plot.data = "mean")) + vdiffr::expect_doppelganger("filter-mspct-median-A", + autoplot(T2A(two_leaves.mspct, action = "replace"), plot.data = "median")) +}) + +test_that("reflector_spct", { + set_annotations_default() + vdiffr::expect_doppelganger("reflector-default-tot-scaled", + autoplot(fscale(Ler_leaf_rflt.spct, target = 0.06, + range = c(400,700), set.scaled = TRUE))) + vdiffr::expect_doppelganger("reflector-default-tot-normalized", + autoplot(normalize(Ler_leaf_rflt.spct, norm = "max"))) + vdiffr::expect_doppelganger("reflector-default-tot-normalized-759", + autoplot(normalize(Ler_leaf_rflt.spct, norm = 759.1))) + + vdiffr::expect_doppelganger("reflector-default-tot", + autoplot(Ler_leaf_rflt.spct)) + vdiffr::expect_doppelganger("reflector-default-tot-ylim", + autoplot(Ler_leaf_rflt.spct, ylim = c(-0.1, 0.65))) + vdiffr::expect_doppelganger("reflector-default-pc-out-tot", + autoplot(Ler_leaf_rflt.spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("reflector-text-size-tot", + autoplot(Ler_leaf_rflt.spct, text.size = 3.5)) + vdiffr::expect_doppelganger("reflector-span-31-tot", + autoplot(Ler_leaf_rflt.spct, span = 31)) + vdiffr::expect_doppelganger("reflector-wb-vis-tot", + autoplot(Ler_leaf_rflt.spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("reflector-label-average-tot", + autoplot(Ler_leaf_rflt.spct, label.qty = "average")) + vdiffr::expect_doppelganger("reflector-label-mean-tot", + autoplot(Ler_leaf_rflt.spct, label.qty = "mean")) + vdiffr::expect_doppelganger("reflector-range-num-tot", + autoplot(Ler_leaf_rflt.spct, range = c(500, 700))) + vdiffr::expect_doppelganger("reflector-range-wb-tot", + autoplot(Ler_leaf_rflt.spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("reflector-no-annotations-tot", + autoplot(Ler_leaf_rflt.spct, annotations = "")) + vdiffr::expect_doppelganger("reflector-minus-annotations-tot", + autoplot(Ler_leaf_rflt.spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("reflector-plus-annotations-tot", + autoplot(Ler_leaf_rflt.spct, annotations = c("+", "boundaries"))) +}) + +test_that("reflector_mspct", { + set_annotations_default() + two_leaves_Rfr.mspct <- reflector_mspct(list(one = Ler_leaf_rflt.spct, + half = Ler_leaf_rflt.spct / 2)) + vdiffr::expect_doppelganger("reflector-mspct-default", + autoplot(two_leaves_Rfr.mspct)) + vdiffr::expect_doppelganger("reflector-mspct-default-range", + autoplot(two_leaves_Rfr.mspct, range = c(500, 700))) + vdiffr::expect_doppelganger("reflector-mspct-no-annotations", + autoplot(two_leaves_Rfr.mspct, annotations = "")) + vdiffr::expect_doppelganger("reflector-mspct-reserve-space", + autoplot(two_leaves_Rfr.mspct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("reflector-mspct-mean", + autoplot(two_leaves_Rfr.mspct, plot.data = "mean")) + vdiffr::expect_doppelganger("reflector-mspct-median", + autoplot(two_leaves_Rfr.mspct, plot.data = "median")) + # triggers warning + # vdiffr::expect_doppelganger("reflector-mspct-sum", + # autoplot(two_leaves_Rfr.mspct, plot.data = "sum")) + testthat::expect_warning(autoplot(two_leaves_Rfr.mspct, plot.data = "sum")) + vdiffr::expect_doppelganger("reflector-mspct-sum", + autoplot(two_leaves_Rfr.mspct, plot.data = "prod")) + vdiffr::expect_doppelganger("reflector-mspct-se", + autoplot(two_leaves_Rfr.mspct, plot.data = "se")) + vdiffr::expect_doppelganger("reflector-mspct-se-ylab", + autoplot(two_leaves_Rfr.mspct, plot.data = "se", ylab = "Standard error of the mean")) + vdiffr::expect_doppelganger("reflector-mspct-var", + autoplot(two_leaves_Rfr.mspct, plot.data = "var")) + vdiffr::expect_doppelganger("reflector-mspct-var-ylab", + autoplot(two_leaves_Rfr.mspct, plot.data = "var", ylab = "Variance")) + vdiffr::expect_doppelganger("reflector-mspct-mean-Tfr", + autoplot(two_leaves_Rfr.mspct, plot.data = "mean")) + vdiffr::expect_doppelganger("reflector-mspct-median-Tfr", + autoplot(two_leaves_Rfr.mspct, plot.data = "median")) +}) + +test_that("object_spct", { + set_annotations_default() + vdiffr::expect_doppelganger("object-default-tot", + autoplot(Ler_leaf.spct)) + vdiffr::expect_doppelganger("object-default-pc-out-tot", + autoplot(Ler_leaf.spct, pc.out = TRUE)) + vdiffr::expect_doppelganger("object-text-size-tot", + autoplot(Ler_leaf.spct, text.size = 3.5)) + vdiffr::expect_doppelganger("object-wb-vis-tot", + autoplot(Ler_leaf.spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("object-range-num-tot", + autoplot(Ler_leaf.spct, range = c(500, 700))) + vdiffr::expect_doppelganger("object-range-wb-tot", + autoplot(Ler_leaf.spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("object-no-annotations-tot", + autoplot(Ler_leaf.spct, annotations = "")) + vdiffr::expect_doppelganger("object-reserve-space-tot", + autoplot(Ler_leaf.spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("object-minus-guide-tot", + autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"))) + vdiffr::expect_doppelganger("object-plus-segments-tot", + autoplot(Ler_leaf.spct, annotations = c("+", "segments"))) + + vdiffr::expect_doppelganger("object-default-stk", + autoplot(Ler_leaf.spct, stacked = FALSE)) + vdiffr::expect_doppelganger("object-default-stk-ylim", + autoplot(Ler_leaf.spct, stacked = FALSE, ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("object-default-pc-out-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, pc.out = TRUE)) + vdiffr::expect_doppelganger("object-text-size-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, text.size = 3.5)) + vdiffr::expect_doppelganger("object-minus-peaks-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("-", "peaks"))) + vdiffr::expect_doppelganger("object-peaks-valleys-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("+", "peaks", "valleys"))) + vdiffr::expect_doppelganger("object-plus-valleys-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("+", "valleys"))) + vdiffr::expect_doppelganger("object-wb-vis-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, w.band = VIS_bands())) + vdiffr::expect_doppelganger("object-range-num-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, range = c(500, 700))) + vdiffr::expect_doppelganger("object-range-wb-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("object-no-annotations-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, annotations = "")) + vdiffr::expect_doppelganger("object-minus-labels-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, annotations = c("-", "labels"))) + vdiffr::expect_doppelganger("object-plus-segments-stk", + autoplot(Ler_leaf.spct, stacked = FALSE, annotations = c("+", "segments"))) +}) diff --git a/tests/testthat/test-autoplot-raw-spct.R b/tests/testthat/test-autoplot-raw-spct.R new file mode 100644 index 00000000..eb78cfa6 --- /dev/null +++ b/tests/testthat/test-autoplot-raw-spct.R @@ -0,0 +1,34 @@ +context("autoplot-raw-cps") +library(ggplot2) +library(photobiology) + +# We prepare shorter data objects for spectra to improve tests' runtime. +# We also make sure no data are exactly at the boundary of the possible range to +# avoid warnings. Such values are physically possible but not measurable. +length.out.spct <- 100L +white_led.raw_spct <- interpolate_spct(photobiology::white_led.raw_spct, + length.out = length.out.spct) + +test_that("raw_spct", { + set_annotations_default() + # skip_on_cran() + vdiffr::expect_doppelganger("raw-default", + autoplot(white_led.raw_spct)) + vdiffr::expect_doppelganger("raw-ylim1", + autoplot(white_led.raw_spct, ylim = c(NA, 9e4))) + vdiffr::expect_doppelganger("raw-ylim2", + autoplot(white_led.raw_spct, ylim = c(-5e3, 9e4))) + vdiffr::expect_doppelganger("raw-range-num", + autoplot(white_led.raw_spct, range = c(500, 700))) + vdiffr::expect_doppelganger("raw-range-wb", + autoplot(white_led.raw_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("raw-no-annotations", + autoplot(white_led.raw_spct, annotations = "")) + vdiffr::expect_doppelganger("raw-reserve-space", + autoplot(white_led.raw_spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("raw-minus-annotations", + autoplot(white_led.raw_spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("raw-plus-annotations", + autoplot(white_led.raw_spct, annotations = c("+", "boundaries"))) +}) + diff --git a/tests/testthat/test-autoplot-response-spct.R b/tests/testthat/test-autoplot-response-spct.R new file mode 100644 index 00000000..7d243708 --- /dev/null +++ b/tests/testthat/test-autoplot-response-spct.R @@ -0,0 +1,168 @@ +context("autoplot-response") +library(photobiology) +library(photobiologyWavebands) + +# We prepare shorter data objects for spectra to improve tests' runtime. +# We also make sure no data are exactly at the boundary of the possible range to +# avoid warnings. Such values are physically possible but not measurable. +length.out.spct <- 100L +ccd.spct <- interpolate_spct(photobiology::ccd.spct, length.out = length.out.spct) + +test_that("response_spct", { + set_annotations_default() + vdiffr::expect_doppelganger("response-default-scaled", + autoplot(fscale(ccd.spct, f = "mean", target = 1))) + + vdiffr::expect_doppelganger("response-default", + autoplot(ccd.spct)) + vdiffr::expect_doppelganger("response-default-ylim", + autoplot(ccd.spct, ylim = c(-0.1, 1.2))) + vdiffr::expect_doppelganger("response-text-size", + autoplot(ccd.spct, text.size = 3.5)) + vdiffr::expect_doppelganger("response-span-31", + autoplot(ccd.spct, span = 31)) + vdiffr::expect_doppelganger("response-wb-vis", + autoplot(ccd.spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("response-label-average", + autoplot(ccd.spct, label.qty = "average")) + vdiffr::expect_doppelganger("response-label-mean", + autoplot(ccd.spct, label.qty = "mean")) + vdiffr::expect_doppelganger("response-label-total", + autoplot(ccd.spct, label.qty = "total")) + vdiffr::expect_doppelganger("response-label-contrib", + autoplot(ccd.spct, label.qty = "contribution")) + vdiffr::expect_doppelganger("response-label-relative", + autoplot(ccd.spct, label.qty = "relative")) + vdiffr::expect_doppelganger("response-range-num", + autoplot(ccd.spct, range = c(300, 700))) + vdiffr::expect_doppelganger("response-range-wb", + autoplot(ccd.spct, range = waveband(c(300, 700)))) + vdiffr::expect_doppelganger("response-no-annotations", + autoplot(ccd.spct, annotations = "")) + vdiffr::expect_doppelganger("response-reserve-space", + autoplot(ccd.spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("response-minus-annotations", + autoplot(ccd.spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("response-plus-annotations", + autoplot(ccd.spct, annotations = c("+", "boundaries"))) + + vdiffr::expect_doppelganger("response-default-q", + autoplot(ccd.spct, unit.out = "photon")) + vdiffr::expect_doppelganger("response-default-ylim-q", + autoplot(ccd.spct, unit.out = "photon", ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("response-text-size-q", + autoplot(ccd.spct, unit.out = "photon", text.size = 3.5)) + vdiffr::expect_doppelganger("response-span-31-q", + autoplot(ccd.spct, unit.out = "photon", span = 31)) + vdiffr::expect_doppelganger("response-wb-vis-q", + autoplot(ccd.spct, unit.out = "photon", w.band = VIS_bands())) + vdiffr::expect_doppelganger("response-label-average-q", + autoplot(ccd.spct, unit.out = "photon", label.qty = "average")) + vdiffr::expect_doppelganger("response-label-mean-q", + autoplot(ccd.spct, unit.out = "photon", label.qty = "mean")) + vdiffr::expect_doppelganger("response-label-total-q", + autoplot(ccd.spct, unit.out = "photon", label.qty = "total")) + vdiffr::expect_doppelganger("response-label-contrib-q", + autoplot(ccd.spct, unit.out = "photon", label.qty = "contribution")) + vdiffr::expect_doppelganger("response-label-relative-q", + autoplot(ccd.spct, unit.out = "photon", label.qty = "relative")) + vdiffr::expect_doppelganger("response-range-num-q", + autoplot(ccd.spct, unit.out = "photon", range = c(500, 700))) + vdiffr::expect_doppelganger("response-range-wb-q", + autoplot(ccd.spct, unit.out = "photon", range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("response-no-annotations-q", + autoplot(ccd.spct, unit.out = "photon", annotations = "")) + vdiffr::expect_doppelganger("response-minus-summaries-q", + autoplot(ccd.spct, unit.out = "photon", annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("response-minus-boxes-q", + autoplot(ccd.spct, unit.out = "photon", annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("response-plus-boundaries-q", + autoplot(ccd.spct, unit.out = "photon", annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("response-plus-segments-q", + autoplot(ccd.spct, unit.out = "photon", annotations = c("+", "segments"))) + + # time units + vdiffr::expect_doppelganger("response-second", + autoplot(setTimeUnit(ccd.spct, "second", TRUE))) + vdiffr::expect_doppelganger("response-hour", + autoplot(setTimeUnit(ccd.spct, "hour", TRUE))) + vdiffr::expect_doppelganger("response-day", + autoplot(setTimeUnit(ccd.spct, "day", TRUE))) + vdiffr::expect_doppelganger("response-exposure", + autoplot(setTimeUnit(ccd.spct, "exposure", TRUE))) + vdiffr::expect_doppelganger("response-duration", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(4.5, "minutes"), TRUE))) + vdiffr::expect_doppelganger("response-none", + autoplot(setTimeUnit(ccd.spct, "unknown", TRUE))) + vdiffr::expect_doppelganger("response-seconds", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "seconds"), TRUE))) + vdiffr::expect_doppelganger("response-hours", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "hours"), TRUE))) + vdiffr::expect_doppelganger("response-days", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "days"), TRUE))) + + vdiffr::expect_doppelganger("response-second-q", + autoplot(setTimeUnit(ccd.spct, "second", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-hour-q", + autoplot(setTimeUnit(ccd.spct, "hour", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-day-q", + autoplot(setTimeUnit(ccd.spct, "day", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-exposure-q", + autoplot(setTimeUnit(ccd.spct, "exposure", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-duration-q", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(4.5, "minutes"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-none-q", + autoplot(setTimeUnit(ccd.spct, "unknown", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-seconds-q", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "seconds"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-hours-q", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "hours"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("response-days-q", + autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "days"), TRUE), unit.out = "photon")) + + }) + +test_that("response_mspct", { + set_annotations_default() + ccd.spct <- interpolate_spct(photobiology::ccd.spct, length.out = length.out.spct) + two_ccds.mspct <- response_mspct(list(one = ccd.spct, + half = ccd.spct / 2)) + + vdiffr::expect_doppelganger("response-mspct-default", + autoplot(two_ccds.mspct)) + vdiffr::expect_doppelganger("response-mspct-default-range", + autoplot(two_ccds.mspct, range = c(500, 700))) + vdiffr::expect_doppelganger("response-mspct-default-e", + autoplot(two_ccds.mspct, unit.out = "energy")) + vdiffr::expect_doppelganger("response-mspct-default-p", + autoplot(two_ccds.mspct, unit.out = "photon")) + vdiffr::expect_doppelganger("response-mspct-no-annotations", + autoplot(two_ccds.mspct, annotations = "")) + vdiffr::expect_doppelganger("response-mspct-reserve-space", + autoplot(two_ccds.mspct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("response-mspct-mean", + autoplot(two_ccds.mspct, plot.data = "mean")) + vdiffr::expect_doppelganger("response-mspct-median", + autoplot(two_ccds.mspct, plot.data = "median")) + vdiffr::expect_doppelganger("response-mspct-sum", + autoplot(two_ccds.mspct, plot.data = "sum")) + # vdiffr::expect_warning("response-mspct-prod", + # autoplot(two_ccds.mspct, plot.data = "prod")) + testthat::expect_warning(autoplot(two_ccds.mspct, plot.data = "prod")) + vdiffr::expect_doppelganger("response-mspct-se", + autoplot(two_ccds.mspct, plot.data = "se")) + vdiffr::expect_doppelganger("response-mspct-se-ylab", + autoplot(two_ccds.mspct, plot.data = "se", ylab = "Standard error of the mean")) + vdiffr::expect_doppelganger("response-mspct-var", + autoplot(two_ccds.mspct, plot.data = "var")) + vdiffr::expect_doppelganger("response-mspct-var-ylab", + autoplot(two_ccds.mspct, plot.data = "var", ylab = "Variance")) + vdiffr::expect_doppelganger("response-mspct-mean-e", + autoplot(two_ccds.mspct, plot.data = "mean", unit.out = "energy")) + vdiffr::expect_doppelganger("response-mspct-mean-p", + autoplot(two_ccds.mspct, plot.data = "mean", unit.out = "photon")) + vdiffr::expect_doppelganger("response-mspct-median-e", + autoplot(two_ccds.mspct, plot.data = "median", unit.out = "energy")) + vdiffr::expect_doppelganger("response-mspct-median-p", + autoplot(two_ccds.mspct, plot.data = "median", unit.out = "photon")) +}) diff --git a/tests/testthat/test-autoplot-source-spct.R b/tests/testthat/test-autoplot-source-spct.R new file mode 100644 index 00000000..27a81c5d --- /dev/null +++ b/tests/testthat/test-autoplot-source-spct.R @@ -0,0 +1,240 @@ +context("autoplot-source") +library(ggplot2) +library(photobiology) +library(photobiologyWavebands) + +# We prepare shorter data objects for spectra to improve tests' runtime. +# We also make sure no data are exactly at the boundary of the possible range to +# avoid warnings. Such values are physically possible but not measurable. +length.out.spct <- 100L +sun.spct <- interpolate_spct(photobiology::sun.spct, length.out = length.out.spct) +white_led.source_spct <- interpolate_spct(photobiology::white_led.source_spct, length.out = length.out.spct) + +test_that("source_spct", { + set_annotations_default() + vdiffr::expect_doppelganger("source-default-scaled", + autoplot(fscale(white_led.source_spct))) + vdiffr::expect_doppelganger("source-default-normalized", + autoplot(normalize(white_led.source_spct))) + vdiffr::expect_doppelganger("source-default-norm-550", + autoplot(normalize(white_led.source_spct, norm = 550))) + + vdiffr::expect_doppelganger("source-default", + autoplot(white_led.source_spct)) + vdiffr::expect_doppelganger("source-default-geom-spct", + autoplot(white_led.source_spct, geom = "spct")) + vdiffr::expect_doppelganger("source-ylim1", + autoplot(white_led.source_spct, ylim = c(NA, 1))) + vdiffr::expect_doppelganger("source-ylim2", + autoplot(white_led.source_spct, ylim = c(-0.1, 1))) + vdiffr::expect_doppelganger("source-text-size", + autoplot(white_led.source_spct, text.size = 3.5)) + vdiffr::expect_doppelganger("source-span-11", + autoplot(white_led.source_spct, span = 11)) + vdiffr::expect_doppelganger("source-wb-vis-1", + autoplot(white_led.source_spct, w.band = VIS())) + vdiffr::expect_doppelganger("source-wb-vis", + autoplot(white_led.source_spct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("source-wb-null", + autoplot(white_led.source_spct, w.band = NULL)) + vdiffr::expect_doppelganger("source-label-average", + autoplot(white_led.source_spct, label.qty = "average")) + vdiffr::expect_doppelganger("source-label-mean", + autoplot(white_led.source_spct, label.qty = "mean")) + vdiffr::expect_doppelganger("source-label-total", + autoplot(white_led.source_spct, label.qty = "total")) + vdiffr::expect_doppelganger("source-label-contrib", + autoplot(white_led.source_spct, label.qty = "contribution")) + vdiffr::expect_doppelganger("source-label-relative", + autoplot(white_led.source_spct, label.qty = "relative")) + vdiffr::expect_doppelganger("source-range-num", + autoplot(white_led.source_spct, range = c(500, 700))) + vdiffr::expect_doppelganger("source-range-wb", + autoplot(white_led.source_spct, range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("source-no-annotations", + autoplot(white_led.source_spct, annotations = "")) + vdiffr::expect_doppelganger("source-reserve-space", + autoplot(white_led.source_spct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("source-minus-annotations", + autoplot(white_led.source_spct, annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("source-plus-annotations", + autoplot(white_led.source_spct, annotations = c("+", "boundaries"))) + + vdiffr::expect_doppelganger("source-default-q-scaled", + autoplot(fscale(white_led.source_spct), unit.out = "photon")) + vdiffr::expect_doppelganger("source-default-q-normalized", + autoplot(normalize(white_led.source_spct), unit.out = "photon")) + + vdiffr::expect_doppelganger("source-default-q", + autoplot(white_led.source_spct, unit.out = "photon")) + vdiffr::expect_doppelganger("source-ylim1-q", + autoplot(white_led.source_spct, unit.out = "photon", ylim = c(NA, 6))) + vdiffr::expect_doppelganger("source-ylim2-q", + autoplot(white_led.source_spct, unit.out = "photon", ylim = c(-0.5, 6))) + vdiffr::expect_doppelganger("source-text-size-q", + autoplot(white_led.source_spct, unit.out = "photon", text.size = 3.5)) + vdiffr::expect_doppelganger("source-span-11-q", + autoplot(white_led.source_spct, unit.out = "photon", span = 11)) + vdiffr::expect_doppelganger("source-wb-vis-q", + autoplot(white_led.source_spct, unit.out = "photon", w.band = VIS_bands())) + vdiffr::expect_doppelganger("source-label-average-q", + autoplot(white_led.source_spct, unit.out = "photon", label.qty = "average")) + vdiffr::expect_doppelganger("source-label-mean-q", + autoplot(white_led.source_spct, unit.out = "photon", label.qty = "mean")) + vdiffr::expect_doppelganger("source-range-num-q", + autoplot(white_led.source_spct, unit.out = "photon", range = c(500, 700))) + vdiffr::expect_doppelganger("source-range-wb-q", + autoplot(white_led.source_spct, unit.out = "photon", range = waveband(c(500, 700)))) + vdiffr::expect_doppelganger("source-no-annotations-q", + autoplot(white_led.source_spct, unit.out = "photon", annotations = "")) + vdiffr::expect_doppelganger("source-minus-summaries-q", + autoplot(white_led.source_spct, unit.out = "photon", annotations = c("-", "summaries"))) + vdiffr::expect_doppelganger("source-minus-boxes-q", + autoplot(white_led.source_spct, unit.out = "photon", annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("source-plus-boundaries-q", + autoplot(white_led.source_spct, unit.out = "photon", annotations = c("+", "boundaries"))) + vdiffr::expect_doppelganger("source-plus-segments-q", + autoplot(white_led.source_spct, unit.out = "photon", annotations = c("+", "segments"))) + + vdiffr::expect_doppelganger("source-normalized", + autoplot(normalize(white_led.source_spct))) + vdiffr::expect_doppelganger("source-normalized-pcout", + autoplot(normalize(white_led.source_spct), pc.out = TRUE)) + vdiffr::expect_doppelganger("source-normalized-wl", + autoplot(normalize(white_led.source_spct, norm = 550))) + vdiffr::expect_doppelganger("source-normalized-wl-pcout", + autoplot(normalize(white_led.source_spct, norm = 550), pc.out = TRUE)) + vdiffr::expect_doppelganger("source-normalized-ylim", + autoplot(normalize(white_led.source_spct), ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("source-scaled", + autoplot(fscale(white_led.source_spct))) + vdiffr::expect_doppelganger("source-scaled-total", + autoplot(fscale(white_led.source_spct, f = "total"))) + vdiffr::expect_doppelganger("source-scaled-mean", + autoplot(fscale(white_led.source_spct, f = "mean"))) + vdiffr::expect_doppelganger("source-scaled-mean-2", + autoplot(fscale(white_led.source_spct, target = 2))) + vdiffr::expect_doppelganger("source-scaled-mean-2-PAR", + autoplot(fscale(white_led.source_spct, target = 2, range = PhR()))) + vdiffr::expect_doppelganger("source-scaled-total-200", + autoplot(fscale(white_led.source_spct, f = "total", target = 200))) + vdiffr::expect_doppelganger("source-scaled-total-200-PAR", + autoplot(fscale(white_led.source_spct, f = "total", target = 200, range = PhR()))) + vdiffr::expect_doppelganger("source-scaled-irrad-200", + autoplot(fscale(white_led.source_spct, f = irrad, target = 200))) + vdiffr::expect_doppelganger("source-scaled-irrad-200-PAR", + autoplot(fscale(white_led.source_spct, f = irrad, target = 200, range = PhR()))) + vdiffr::expect_doppelganger("source-product-wb", + autoplot(sun.spct * Red())) + vdiffr::expect_doppelganger("source-product-BSWF", + autoplot(sun.spct * CIE())) + vdiffr::expect_doppelganger("source-product-BSWF-wl", + autoplot(sun.spct * CIE(300))) + # time units + vdiffr::expect_doppelganger("source-second", + autoplot(setTimeUnit(white_led.source_spct, "second", TRUE))) + vdiffr::expect_doppelganger("source-hour", + autoplot(setTimeUnit(white_led.source_spct, "hour", TRUE))) + vdiffr::expect_doppelganger("source-day", + autoplot(setTimeUnit(white_led.source_spct, "day", TRUE))) + vdiffr::expect_doppelganger("source-exposure", + autoplot(setTimeUnit(white_led.source_spct, "exposure", TRUE))) + vdiffr::expect_doppelganger("source-duration", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(4.5, "minutes"), TRUE))) + vdiffr::expect_doppelganger("source-none", + autoplot(setTimeUnit(white_led.source_spct, "unknown", TRUE))) + vdiffr::expect_doppelganger("source-seconds", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "seconds"), TRUE))) + vdiffr::expect_doppelganger("source-hours", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "hours"), TRUE))) + vdiffr::expect_doppelganger("source-days", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "days"), TRUE))) + + vdiffr::expect_doppelganger("source-second-q", + autoplot(setTimeUnit(white_led.source_spct, "second", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-hour-q", + autoplot(setTimeUnit(white_led.source_spct, "hour", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-day-q", + autoplot(setTimeUnit(white_led.source_spct, "day", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-exposure-q", + autoplot(setTimeUnit(white_led.source_spct, "exposure", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-duration-q", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(4.5, "minutes"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-none-q", + autoplot(setTimeUnit(white_led.source_spct, "unknown", TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-seconds-q", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "seconds"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-hours-q", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "hours"), TRUE), unit.out = "photon")) + vdiffr::expect_doppelganger("source-days-q", + autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "days"), TRUE), unit.out = "photon")) + + }) + +test_that("source_mspct", { + set_annotations_default() + white_led.source_spct <- interpolate_spct(photobiology::white_led.source_spct, length.out = length.out.spct) + two_leds.mspct <- source_mspct(list(one = white_led.source_spct, + half = white_led.source_spct / 2)) + + vdiffr::expect_doppelganger("source-mspct-default", + autoplot(two_leds.mspct)) + vdiffr::expect_doppelganger("source-mspct-default-idfactor", + autoplot(two_leds.mspct, idfactor = "spectrum")) + vdiffr::expect_doppelganger("source-mspct-default-geom-spct", + autoplot(two_leds.mspct, geom = "spct")) + vdiffr::expect_doppelganger("source-mspct-ylim", + autoplot(two_leds.mspct, ylim = c(-0.1, 1.2))) + vdiffr::expect_doppelganger("source-mspct-default-range", + autoplot(two_leds.mspct, range = c(500, 700))) + vdiffr::expect_doppelganger("source-mspct-default-wband-wb", + autoplot(two_leds.mspct, w.band = VIS())) + vdiffr::expect_doppelganger("source-mspct-default-wband-wbls", + autoplot(two_leds.mspct, w.band = VIS_bands())) + vdiffr::expect_doppelganger("source-mspct-default-wband-null", + autoplot(two_leds.mspct, w.band = NULL)) + vdiffr::expect_doppelganger("source-mspct-default-e", + autoplot(two_leds.mspct, unit.out = "energy")) + vdiffr::expect_doppelganger("source-mspct-default-p", + autoplot(two_leds.mspct, unit.out = "photon")) + vdiffr::expect_doppelganger("source-mspct-no-annotations", + autoplot(two_leds.mspct, annotations = "")) + vdiffr::expect_doppelganger("source-mspct-reserve-space", + autoplot(two_leds.mspct, annotations = "reserve.space")) + vdiffr::expect_doppelganger("source-mspct-mean", + autoplot(two_leds.mspct, plot.data = "mean")) + vdiffr::expect_doppelganger("source-mspct-median", + autoplot(two_leds.mspct, plot.data = "median")) + vdiffr::expect_doppelganger("source-mspct-sum", + autoplot(two_leds.mspct, plot.data = "sum")) + # triggers warning + # vdiffr::expect_doppelganger("source-mspct-sum", + # autoplot(two_leds.mspct, plot.data = "prod")) + testthat::expect_warning(autoplot(two_leds.mspct, plot.data = "prod")) + vdiffr::expect_doppelganger("source-mspct-se", + autoplot(two_leds.mspct, plot.data = "se")) + vdiffr::expect_doppelganger("source-mspct-se-ylab", + autoplot(two_leds.mspct, plot.data = "se", ylab = "Standard error of the mean")) + vdiffr::expect_doppelganger("source-mspct-var", + autoplot(two_leds.mspct, plot.data = "var")) + vdiffr::expect_doppelganger("source-mspct-var-ylab", + autoplot(two_leds.mspct, plot.data = "var", ylab = "Variance")) + vdiffr::expect_doppelganger("source-mspct-mean-e", + autoplot(two_leds.mspct, plot.data = "mean", unit.out = "energy")) + vdiffr::expect_doppelganger("source-mspct-median-e", + autoplot(two_leds.mspct, plot.data = "median", unit.out = "energy")) + vdiffr::expect_doppelganger("source-mspct-mean-p", + autoplot(two_leds.mspct, plot.data = "mean", unit.out = "photon")) + vdiffr::expect_doppelganger("source-mspct-median-p", + autoplot(two_leds.mspct, plot.data = "median", unit.out = "photon")) + + vdiffr::expect_doppelganger("source-mspct-facets1", + autoplot(two_leds.mspct, facets = 1)) + vdiffr::expect_doppelganger("source-mspct-facets2", + autoplot(two_leds.mspct, facets = 2)) + vdiffr::expect_doppelganger("source-mspct-facetsT", + autoplot(two_leds.mspct, facets = TRUE)) + vdiffr::expect_doppelganger("source-mspct-facetsT-geom-spct", + autoplot(two_leds.mspct, facets = TRUE, geom = "spct")) + +}) diff --git a/tests/testthat/test-autoplot-waveband.R b/tests/testthat/test-autoplot-waveband.R new file mode 100644 index 00000000..d9b81a40 --- /dev/null +++ b/tests/testthat/test-autoplot-waveband.R @@ -0,0 +1,23 @@ +context("autoplot-waveband") +library(ggplot2) +library(photobiology) + +test_that("waveband", { + set_annotations_default() + vdiffr::expect_doppelganger("waveband-default-cie", + autoplot(CIE(), range = c(230, 430))) + vdiffr::expect_doppelganger("waveband-default-red", + autoplot(Red())) + vdiffr::expect_doppelganger("waveband-default-ylim", + autoplot(Red(), ylim = c(-0.2, 1.2))) + vdiffr::expect_doppelganger("waveband-text-size", + autoplot(Red(), text.size = 3.5)) + vdiffr::expect_doppelganger("waveband-plus-segments", + autoplot(Red(), annotations = c("+", "segments"))) + vdiffr::expect_doppelganger("waveband-minus-boxes", + autoplot(Red(), annotations = c("-", "boxes"))) + vdiffr::expect_doppelganger("waveband-no-annotations", + autoplot(Red(), annotations = "")) + vdiffr::expect_doppelganger("waveband-reserve-space", + autoplot(Red(), annotations = "reserve.space")) +}) diff --git a/tests/testthat/test-plot-methods.R b/tests/testthat/test-plot-methods.R deleted file mode 100644 index 5bb3a6c1..00000000 --- a/tests/testthat/test-plot-methods.R +++ /dev/null @@ -1,1004 +0,0 @@ -context("plot") -library(ggplot2) -library(photobiology) -library(photobiologyWavebands) - -# We prepare shorter data objects for spectra to improve tests' runtime. -# We also make sure no data are exactly at the boundary of the possible range to -# avoid warnings. Such values are physically possible but not measurable. -length.out.spct <- 100L -sun.spct <- interpolate_spct(photobiology::sun.spct, length.out = length.out.spct) -white_led.raw_spct <- interpolate_spct(photobiology::white_led.raw_spct, length.out = length.out.spct) -white_led.cps_spct <- interpolate_spct(photobiology::white_led.cps_spct, length.out = length.out.spct) -white_led.source_spct <- interpolate_spct(photobiology::white_led.source_spct, length.out = length.out.spct) -Ler_leaf_trns.spct <- interpolate_spct(photobiology::Ler_leaf_trns.spct, length.out = length.out.spct) -Ler_leaf_trns.spct <- clean(Ler_leaf_trns.spct, range.s.data = c(1e-5, 1 - 1e-5)) -Ler_leaf_trns_i.spct <- interpolate_spct(photobiology::Ler_leaf_trns_i.spct, length.out = length.out.spct) -Ler_leaf_trns_i.spct <- clean(Ler_leaf_trns_i.spct, range.s.data = c(1e-5, 1 - 1e-5)) -Ler_leaf_rflt.spct <- interpolate_spct(photobiology::Ler_leaf_rflt.spct, length.out = length.out.spct) -Ler_leaf_rflt.spct <- clean(Ler_leaf_rflt.spct, range.s.data = c(1e-5, 1 - 1e-5)) -Ler_leaf.spct <- clean(Ler_leaf.spct, min.Afr = 1e-5, range.s.data = c(1e-5, 1 - 1e-5)) -Ler_leaf.spct <- interpolate_spct(photobiology::Ler_leaf.spct, length.out = length.out.spct) -Ler_leaf.spct <- clean(Ler_leaf.spct, min.Afr = 1e-5, range.s.data = c(1e-5, 1 - 1e-5)) -ccd.spct <- interpolate_spct(photobiology::ccd.spct, length.out = length.out.spct) - -test_that("raw_spct", { - set_annotations_default() - # skip_on_cran() - vdiffr::expect_doppelganger("raw-default", - autoplot(white_led.raw_spct)) - vdiffr::expect_doppelganger("raw-ylim1", - autoplot(white_led.raw_spct, ylim = c(NA, 9e4))) - vdiffr::expect_doppelganger("raw-ylim2", - autoplot(white_led.raw_spct, ylim = c(-5e3, 9e4))) - vdiffr::expect_doppelganger("raw-range-num", - autoplot(white_led.raw_spct, range = c(500, 700))) - vdiffr::expect_doppelganger("raw-range-wb", - autoplot(white_led.raw_spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("raw-no-annotations", - autoplot(white_led.raw_spct, annotations = "")) - vdiffr::expect_doppelganger("raw-reserve-space", - autoplot(white_led.raw_spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("raw-minus-annotations", - autoplot(white_led.raw_spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("raw-plus-annotations", - autoplot(white_led.raw_spct, annotations = c("+", "boundaries"))) -}) - -test_that("cps_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("cps-default", - autoplot(white_led.cps_spct)) - vdiffr::expect_doppelganger("cps-ylim1", - autoplot(white_led.cps_spct, ylim = c(NA, 5e5))) - vdiffr::expect_doppelganger("cps-ylim2", - autoplot(white_led.cps_spct, ylim = c(-1e5, 5e5))) - vdiffr::expect_doppelganger("cps-range-num", - autoplot(white_led.cps_spct, range = c(500, 700))) - vdiffr::expect_doppelganger("cps-range-wb", - autoplot(white_led.cps_spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("cps-no-annotations", - autoplot(white_led.cps_spct, annotations = "")) - vdiffr::expect_doppelganger("cps-reserve-space", - autoplot(white_led.cps_spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("cps-minus-annotations", - autoplot(white_led.cps_spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("cps-plus-annotations", - autoplot(white_led.cps_spct, annotations = c("+", "boundaries"))) -}) - -test_that("source_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("source-default-scaled", - autoplot(fscale(white_led.source_spct))) - vdiffr::expect_doppelganger("source-default-normalized", - autoplot(normalize(white_led.source_spct))) - vdiffr::expect_doppelganger("source-default-norm-550", - autoplot(white_led.source_spct, norm = 550)) - - vdiffr::expect_doppelganger("source-default", - autoplot(white_led.source_spct)) - vdiffr::expect_doppelganger("source-ylim1", - autoplot(white_led.source_spct, ylim = c(NA, 1))) - vdiffr::expect_doppelganger("source-ylim2", - autoplot(white_led.source_spct, ylim = c(-0.1, 1))) - vdiffr::expect_doppelganger("source-text-size", - autoplot(white_led.source_spct, text.size = 3.5)) - vdiffr::expect_doppelganger("source-span-31", - autoplot(white_led.source_spct, span = 31)) - vdiffr::expect_doppelganger("source-wb-vis", - autoplot(white_led.source_spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("source-label-average", - autoplot(white_led.source_spct, label.qty = "average")) - vdiffr::expect_doppelganger("source-label-mean", - autoplot(white_led.source_spct, label.qty = "mean")) - vdiffr::expect_doppelganger("source-label-total", - autoplot(white_led.source_spct, label.qty = "total")) - vdiffr::expect_doppelganger("source-label-contrib", - autoplot(white_led.source_spct, label.qty = "contribution")) - vdiffr::expect_doppelganger("source-label-relative", - autoplot(white_led.source_spct, label.qty = "relative")) - vdiffr::expect_doppelganger("source-range-num", - autoplot(white_led.source_spct, range = c(500, 700))) - vdiffr::expect_doppelganger("source-range-wb", - autoplot(white_led.source_spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("source-no-annotations", - autoplot(white_led.source_spct, annotations = "")) - vdiffr::expect_doppelganger("source-reserve-space", - autoplot(white_led.source_spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("source-minus-annotations", - autoplot(white_led.source_spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("source-plus-annotations", - autoplot(white_led.source_spct, annotations = c("+", "boundaries"))) - - vdiffr::expect_doppelganger("source-default-q-scaled", - autoplot(fscale(white_led.source_spct), unit.out = "photon")) - vdiffr::expect_doppelganger("source-default-q-normalized", - autoplot(normalize(white_led.source_spct), unit.out = "photon")) - - vdiffr::expect_doppelganger("source-default-q", - autoplot(white_led.source_spct, unit.out = "photon")) - vdiffr::expect_doppelganger("source-ylim1-q", - autoplot(white_led.source_spct, unit.out = "photon", ylim = c(NA, 6))) - vdiffr::expect_doppelganger("source-ylim2-q", - autoplot(white_led.source_spct, unit.out = "photon", ylim = c(-0.5, 6))) - vdiffr::expect_doppelganger("source-text-size-q", - autoplot(white_led.source_spct, unit.out = "photon", text.size = 3.5)) - vdiffr::expect_doppelganger("source-span-31-q", - autoplot(white_led.source_spct, unit.out = "photon", span = 31)) - vdiffr::expect_doppelganger("source-wb-vis-q", - autoplot(white_led.source_spct, unit.out = "photon", w.band = VIS_bands())) - vdiffr::expect_doppelganger("source-label-average-q", - autoplot(white_led.source_spct, unit.out = "photon", label.qty = "average")) - vdiffr::expect_doppelganger("source-label-mean-q", - autoplot(white_led.source_spct, unit.out = "photon", label.qty = "mean")) - vdiffr::expect_doppelganger("source-range-num-q", - autoplot(white_led.source_spct, unit.out = "photon", range = c(500, 700))) - vdiffr::expect_doppelganger("source-range-wb-q", - autoplot(white_led.source_spct, unit.out = "photon", range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("source-no-annotations-q", - autoplot(white_led.source_spct, unit.out = "photon", annotations = "")) - vdiffr::expect_doppelganger("source-minus-summaries-q", - autoplot(white_led.source_spct, unit.out = "photon", annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("source-minus-boxes-q", - autoplot(white_led.source_spct, unit.out = "photon", annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("source-plus-boundaries-q", - autoplot(white_led.source_spct, unit.out = "photon", annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("source-plus-segments-q", - autoplot(white_led.source_spct, unit.out = "photon", annotations = c("+", "segments"))) - - vdiffr::expect_doppelganger("source-normalized", - autoplot(normalize(white_led.source_spct))) - vdiffr::expect_doppelganger("source-normalized-wl", - autoplot(normalize(white_led.source_spct, norm = 550))) - vdiffr::expect_doppelganger("source-normalized-ylim", - autoplot(normalize(white_led.source_spct), ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("source-scaled", - autoplot(fscale(white_led.source_spct))) - vdiffr::expect_doppelganger("source-scaled-total", - autoplot(fscale(white_led.source_spct, f = "total"))) - vdiffr::expect_doppelganger("source-scaled-mean", - autoplot(fscale(white_led.source_spct, f = "mean"))) - vdiffr::expect_doppelganger("source-scaled-mean-2", - autoplot(fscale(white_led.source_spct, target = 2))) - vdiffr::expect_doppelganger("source-scaled-mean-2-PAR", - autoplot(fscale(white_led.source_spct, target = 2, range = PhR()))) - vdiffr::expect_doppelganger("source-scaled-total-200", - autoplot(fscale(white_led.source_spct, f = "total", target = 200))) - vdiffr::expect_doppelganger("source-scaled-total-200-PAR", - autoplot(fscale(white_led.source_spct, f = "total", target = 200, range = PAR()))) - vdiffr::expect_doppelganger("source-scaled-irrad-200", - autoplot(fscale(white_led.source_spct, f = irrad, target = 200))) - vdiffr::expect_doppelganger("source-scaled-irrad-200-PAR", - autoplot(fscale(white_led.source_spct, f = irrad, target = 200, range = PhR()))) - vdiffr::expect_doppelganger("source-product-wb", - autoplot(sun.spct * Red())) - vdiffr::expect_doppelganger("source-product-BSWF", - autoplot(sun.spct * CIE())) - vdiffr::expect_doppelganger("source-product-BSWF-wl", - autoplot(sun.spct * CIE(300))) - # time units - vdiffr::expect_doppelganger("source-second", - autoplot(setTimeUnit(white_led.source_spct, "second", TRUE))) - vdiffr::expect_doppelganger("source-hour", - autoplot(setTimeUnit(white_led.source_spct, "hour", TRUE))) - vdiffr::expect_doppelganger("source-day", - autoplot(setTimeUnit(white_led.source_spct, "day", TRUE))) - vdiffr::expect_doppelganger("source-exposure", - autoplot(setTimeUnit(white_led.source_spct, "exposure", TRUE))) - vdiffr::expect_doppelganger("source-duration", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(4.5, "minutes"), TRUE))) - vdiffr::expect_doppelganger("source-none", - autoplot(setTimeUnit(white_led.source_spct, "unknown", TRUE))) - vdiffr::expect_doppelganger("source-seconds", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "seconds"), TRUE))) - vdiffr::expect_doppelganger("source-hours", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "hours"), TRUE))) - vdiffr::expect_doppelganger("source-days", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "days"), TRUE))) - - vdiffr::expect_doppelganger("source-second-q", - autoplot(setTimeUnit(white_led.source_spct, "second", TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-hour-q", - autoplot(setTimeUnit(white_led.source_spct, "hour", TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-day-q", - autoplot(setTimeUnit(white_led.source_spct, "day", TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-exposure-q", - autoplot(setTimeUnit(white_led.source_spct, "exposure", TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-duration-q", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(4.5, "minutes"), TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-none-q", - autoplot(setTimeUnit(white_led.source_spct, "unknown", TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-seconds-q", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "seconds"), TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-hours-q", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "hours"), TRUE), unit.out = "photon")) - vdiffr::expect_doppelganger("source-days-q", - autoplot(setTimeUnit(white_led.source_spct, lubridate::duration(1, "days"), TRUE), unit.out = "photon")) - - }) - -test_that("source_mspct", { - set_annotations_default() - two_leds.mspct <- source_mspct(list(one = white_led.source_spct, - half = white_led.source_spct / 2)) - - vdiffr::expect_doppelganger("source-mspct-default", - autoplot(two_leds.mspct)) - vdiffr::expect_doppelganger("source-mspct-ylim", - autoplot(two_leds.mspct, ylim = c(-0.1, 1.2))) - vdiffr::expect_doppelganger("source-mspct-default-range", - autoplot(two_leds.mspct, range = c(500, 700))) - vdiffr::expect_doppelganger("source-mspct-default-e", - autoplot(two_leds.mspct, unit.out = "energy")) - vdiffr::expect_doppelganger("source-mspct-default-p", - autoplot(two_leds.mspct, unit.out = "photon")) - vdiffr::expect_doppelganger("source-mspct-no-annotations", - autoplot(two_leds.mspct, annotations = "")) - vdiffr::expect_doppelganger("source-mspct-reserve-space", - autoplot(two_leds.mspct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("source-mspct-mean", - autoplot(two_leds.mspct, plot.data = "mean")) - vdiffr::expect_doppelganger("source-mspct-median", - autoplot(two_leds.mspct, plot.data = "median")) - vdiffr::expect_doppelganger("source-mspct-sum", - autoplot(two_leds.mspct, plot.data = "sum")) - # triggers warning - # vdiffr::expect_doppelganger("source-mspct-sum", - # autoplot(two_leds.mspct, plot.data = "prod")) - testthat::expect_warning(autoplot(two_leds.mspct, plot.data = "prod")) - vdiffr::expect_doppelganger("source-mspct-se", - autoplot(two_leds.mspct, plot.data = "se")) - vdiffr::expect_doppelganger("source-mspct-se-ylab", - autoplot(two_leds.mspct, plot.data = "se", ylab = "Standard error of the mean")) - vdiffr::expect_doppelganger("source-mspct-var", - autoplot(two_leds.mspct, plot.data = "var")) - vdiffr::expect_doppelganger("source-mspct-var-ylab", - autoplot(two_leds.mspct, plot.data = "var", ylab = "Variance")) - vdiffr::expect_doppelganger("source-mspct-mean-e", - autoplot(two_leds.mspct, plot.data = "mean", unit.out = "energy")) - vdiffr::expect_doppelganger("source-mspct-median-e", - autoplot(two_leds.mspct, plot.data = "median", unit.out = "energy")) - vdiffr::expect_doppelganger("source-mspct-mean-p", - autoplot(two_leds.mspct, plot.data = "mean", unit.out = "photon")) - vdiffr::expect_doppelganger("source-mspct-median-p", - autoplot(two_leds.mspct, plot.data = "median", unit.out = "photon")) -}) - -test_that("filter_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("filter-default-tot-scaled", - autoplot(fscale(Ler_leaf_trns.spct, target = 0.06, - range = c(400,700), set.scaled = TRUE))) - vdiffr::expect_doppelganger("filter-default-tot-normalized", - autoplot(normalize(Ler_leaf_trns.spct, norm = "max"))) - - vdiffr::expect_doppelganger("filter-default-tot", - autoplot(Ler_leaf_trns.spct)) - vdiffr::expect_doppelganger("filter-default-tot-ylim", - autoplot(Ler_leaf_trns.spct, ylim = c(-0.05, 0.5))) - vdiffr::expect_doppelganger("filter-default-pc-out-tot", - autoplot(Ler_leaf_trns.spct, pc.out = TRUE)) - vdiffr::expect_doppelganger("filter-text-size-tot", - autoplot(Ler_leaf_trns.spct, text.size = 3.5)) - vdiffr::expect_doppelganger("filter-span-31-tot", - autoplot(Ler_leaf_trns.spct, span = 31)) - vdiffr::expect_doppelganger("filter-wb-vis-tot", - autoplot(Ler_leaf_trns.spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("filter-label-average-tot", - autoplot(Ler_leaf_trns.spct, label.qty = "average")) - vdiffr::expect_doppelganger("filter-label-mean-tot", - autoplot(Ler_leaf_trns.spct, label.qty = "mean")) - vdiffr::expect_doppelganger("filter-range-num-tot", - autoplot(Ler_leaf_trns.spct, range = c(500, 700))) - vdiffr::expect_doppelganger("filter-range-wb-tot", - autoplot(Ler_leaf_trns.spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("filter-no-annotations-tot", - autoplot(Ler_leaf_trns.spct, annotations = "")) - vdiffr::expect_doppelganger("filter-minus-annotations-tot", - autoplot(Ler_leaf_trns.spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("filter-plus-annotations-tot", - autoplot(Ler_leaf_trns.spct, annotations = c("+", "boundaries"))) - - vdiffr::expect_doppelganger("filter-default-scaled", - autoplot(fscale(Ler_leaf_trns_i.spct, target = 0.06, - range = c(400,700), set.scaled = TRUE))) - vdiffr::expect_doppelganger("filter-default-normalized", - autoplot(normalize(Ler_leaf_trns_i.spct, norm = "max"))) - vdiffr::expect_doppelganger("filter-default-norm-max", - autoplot(Ler_leaf_trns_i.spct, norm = "max")) - - vdiffr::expect_doppelganger("filter-default", - autoplot(Ler_leaf_trns_i.spct)) - vdiffr::expect_doppelganger("filter-default-ylim", - autoplot(Ler_leaf_trns_i.spct, ylim = c(NA, 1.2))) - vdiffr::expect_doppelganger("filter-default-pc-out", - autoplot(Ler_leaf_trns_i.spct, pc.out = TRUE)) - vdiffr::expect_doppelganger("filter-text-size", - autoplot(Ler_leaf_trns_i.spct, text.size = 3.5)) - vdiffr::expect_doppelganger("filter-span-31", - autoplot(Ler_leaf_trns_i.spct, span = 31)) - vdiffr::expect_doppelganger("filter-wb-vis", - autoplot(Ler_leaf_trns_i.spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("filter-label-average", - autoplot(Ler_leaf_trns_i.spct, label.qty = "average")) - vdiffr::expect_doppelganger("filter-label-mean", - autoplot(Ler_leaf_trns_i.spct, label.qty = "mean")) - vdiffr::expect_doppelganger("filter-range-num", - autoplot(Ler_leaf_trns_i.spct, range = c(500, 700))) - vdiffr::expect_doppelganger("filter-range-wb", - autoplot(Ler_leaf_trns_i.spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("filter-no-annotations", - autoplot(Ler_leaf_trns_i.spct, annotations = "")) - vdiffr::expect_doppelganger("filter-reserve-space", - autoplot(Ler_leaf_trns_i.spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("filter-minus-summaries", - autoplot(Ler_leaf_trns_i.spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("filter-minus-boxes", - autoplot(Ler_leaf_trns_i.spct, annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("filter-plus-boundaries", - autoplot(Ler_leaf_trns_i.spct, annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("filter-plus-segments", - autoplot(Ler_leaf_trns_i.spct, annotations = c("+", "segments"))) - - vdiffr::expect_doppelganger("filter-default-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance")) - vdiffr::expect_doppelganger("filter-default-apt-ylim", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", ylim = c(-0.1, 1.2))) - vdiffr::expect_doppelganger("filter-default-pc-out-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", pc.out = TRUE)) - vdiffr::expect_doppelganger("filter-text-size-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", text.size = 3.5)) - vdiffr::expect_doppelganger("filter-span-31-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", span = 31)) - vdiffr::expect_doppelganger("filter-wb-vis-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", w.band = VIS_bands())) - vdiffr::expect_doppelganger("filter-label-average-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", label.qty = "average")) - vdiffr::expect_doppelganger("filter-label-mean-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", label.qty = "mean")) - vdiffr::expect_doppelganger("filter-range-num-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", range = c(500, 700))) - vdiffr::expect_doppelganger("filter-range-wb-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("filter-no-annotations-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", annotations = "")) - vdiffr::expect_doppelganger("filter-minus-summaries-q", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("filter-minus-boxes-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("filter-plus-boundaries-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("filter-plus-segments-apt", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorptance", annotations = c("+", "segments"))) - - vdiffr::expect_doppelganger("filter-default-a-scaled", - autoplot(fscale(Ler_leaf_trns_i.spct, target = 2, qty.out = "absorbance", - range = c(400,700), set.scaled = TRUE), - plot.qty = "absorbance", range = c(300, NA))) - # vdiffr::expect_doppelganger("filter-default-a-normalized", - # autoplot(normalize(Ler_leaf_trns_i.spct, norm = "max"), - # plot.qty = "absorbance", range = c(300, NA))) - - vdiffr::expect_doppelganger("filter-default-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA))) - vdiffr::expect_doppelganger("filter-default-a-ylim", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), ylim = c(-0.2, 4))) - vdiffr::expect_doppelganger("filter-text-size-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), text.size = 3.5)) - vdiffr::expect_doppelganger("filter-span-31-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), span = 31)) - vdiffr::expect_doppelganger("filter-wb-vis-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), w.band = VIS_bands())) - vdiffr::expect_doppelganger("filter-label-average-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), label.qty = "average")) - vdiffr::expect_doppelganger("filter-label-mean-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), label.qty = "mean")) - vdiffr::expect_doppelganger("filter-range-wb-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("filter-no-annotations-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), annotations = "")) - vdiffr::expect_doppelganger("filter-minus-summaries-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("filter-minus-boxes-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("filter-plus-boundaries-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("filter-plus-segments-a", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "absorbance", range = c(300, NA), annotations = c("+", "segments"))) - - vdiffr::expect_doppelganger("filter-default-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance")) - vdiffr::expect_doppelganger("filter-default-tfr-ylim", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("filter-default-pc-out-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", pc.out = TRUE)) - vdiffr::expect_doppelganger("filter-text-size-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", text.size = 3.5)) - vdiffr::expect_doppelganger("filter-span-31-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", span = 31)) - vdiffr::expect_doppelganger("filter-wb-vis-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", w.band = VIS_bands())) - vdiffr::expect_doppelganger("filter-label-average-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", label.qty = "average")) - vdiffr::expect_doppelganger("filter-label-mean-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", label.qty = "mean")) - vdiffr::expect_doppelganger("filter-range-num-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", range = c(500, 700))) - vdiffr::expect_doppelganger("filter-range-wb-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("filter-no-annotations-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", annotations = "")) - vdiffr::expect_doppelganger("filter-minus-summaries-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("filter-minus-boxes-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("filter-plus-boundaries-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("filter-plus-segments-tfr", - autoplot(Ler_leaf_trns_i.spct, plot.qty = "transmittance", annotations = c("+", "segments"))) -}) - -test_that("filter_mspct", { - set_annotations_default() - two_leaves.mspct <- filter_mspct(list(one = Ler_leaf_trns_i.spct, - half = Ler_leaf_trns_i.spct / 2)) - vdiffr::expect_doppelganger("filter-mspct-default", - autoplot(two_leaves.mspct)) - vdiffr::expect_doppelganger("filter-mspct-default-ylim", - autoplot(two_leaves.mspct, ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("filter-mspct-default-range", - autoplot(two_leaves.mspct, range = c(500, 700))) - # use range to avoid Tfr == 0 values. - vdiffr::expect_doppelganger("filter-mspct-default-A", - autoplot(two_leaves.mspct, - range = c(400,750), - plot.qty = "absorbance")) - vdiffr::expect_doppelganger("filter-mspct-default-Afr", - autoplot(two_leaves.mspct, - range = c(400,750), - plot.qty = "absorptance")) - vdiffr::expect_doppelganger("filter-mspct-default-Tfr", - autoplot(two_leaves.mspct, plot.qty = "transmittance")) - vdiffr::expect_doppelganger("filter-mspct-no-annotations", - autoplot(two_leaves.mspct, annotations = "")) - vdiffr::expect_doppelganger("filter-mspct-reserve-space", - autoplot(two_leaves.mspct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("filter-mspct-mean", - autoplot(two_leaves.mspct, plot.data = "mean")) - vdiffr::expect_doppelganger("filter-mspct-median", - autoplot(two_leaves.mspct, plot.data = "median")) - # triggers warning - # vdiffr::expect_doppelganger("filter-mspct-sum", - # autoplot(two_leaves.mspct, plot.data = "sum")) - testthat::expect_warning(autoplot(two_leaves.mspct, plot.data = "sum")) - vdiffr::expect_doppelganger("filter-mspct-sum", - autoplot(two_leaves.mspct, plot.data = "prod")) - vdiffr::expect_doppelganger("filter-mspct-se", - autoplot(two_leaves.mspct, plot.data = "se")) - vdiffr::expect_doppelganger("filter-mspct-se-ylab", - autoplot(two_leaves.mspct, plot.data = "se", ylab = "Standard error of the mean")) - vdiffr::expect_doppelganger("filter-mspct-var", - autoplot(two_leaves.mspct, plot.data = "var")) - vdiffr::expect_doppelganger("filter-mspct-var-ylab", - autoplot(two_leaves.mspct, plot.data = "var", ylab = "Variance")) - vdiffr::expect_doppelganger("filter-mspct-mean-Tfr", - autoplot(two_leaves.mspct, plot.data = "mean", plot.qty = "transmittance")) - vdiffr::expect_doppelganger("filter-mspct-median-Tfr", - autoplot(two_leaves.mspct, plot.data = "median", plot.qty = "transmittance")) - # Bug in photobiology::rowwise_filter() (fixed in photobiology >= 0.10.11) - # vdiffr::expect_doppelganger("filter-mspct-mean-Afr", - # autoplot(two_leaves.mspct, plot.data = "mean", plot.qty = "absorptance")) - # vdiffr::expect_doppelganger("filter-mspct-median-Afr", - # autoplot(two_leaves.mspct, plot.data = "median", plot.qty = "absorptance")) - vdiffr::expect_doppelganger("filter-mspct-mean-A", - autoplot(two_leaves.mspct, plot.data = "mean", plot.qty = "absorbance")) - vdiffr::expect_doppelganger("filter-mspct-median-A", - autoplot(two_leaves.mspct, plot.data = "median", plot.qty = "absorbance")) -}) - -test_that("reflector_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("reflector-default-tot-scaled", - autoplot(fscale(Ler_leaf_rflt.spct, target = 0.06, - range = c(400,700), set.scaled = TRUE))) - vdiffr::expect_doppelganger("reflector-default-tot-normalized", - autoplot(normalize(Ler_leaf_rflt.spct, norm = "max"))) - vdiffr::expect_doppelganger("reflector-default-tot-norm-max", - autoplot(Ler_leaf_rflt.spct, norm = "max")) - vdiffr::expect_doppelganger("reflector-default-tot-norm-update", - autoplot(Ler_leaf_rflt.spct, norm = "update")) - vdiffr::expect_doppelganger("reflector-default-tot-norm-skip", - autoplot(Ler_leaf_rflt.spct, norm = "skip")) - - vdiffr::expect_doppelganger("reflector-default-tot", - autoplot(Ler_leaf_rflt.spct)) - vdiffr::expect_doppelganger("reflector-default-tot-ylim", - autoplot(Ler_leaf_rflt.spct, ylim = c(-0.1, 0.65))) - vdiffr::expect_doppelganger("reflector-default-pc-out-tot", - autoplot(Ler_leaf_rflt.spct, pc.out = TRUE)) - vdiffr::expect_doppelganger("reflector-text-size-tot", - autoplot(Ler_leaf_rflt.spct, text.size = 3.5)) - vdiffr::expect_doppelganger("reflector-span-31-tot", - autoplot(Ler_leaf_rflt.spct, span = 31)) - vdiffr::expect_doppelganger("reflector-wb-vis-tot", - autoplot(Ler_leaf_rflt.spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("reflector-label-average-tot", - autoplot(Ler_leaf_rflt.spct, label.qty = "average")) - vdiffr::expect_doppelganger("reflector-label-mean-tot", - autoplot(Ler_leaf_rflt.spct, label.qty = "mean")) - vdiffr::expect_doppelganger("reflector-range-num-tot", - autoplot(Ler_leaf_rflt.spct, range = c(500, 700))) - vdiffr::expect_doppelganger("reflector-range-wb-tot", - autoplot(Ler_leaf_rflt.spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("reflector-no-annotations-tot", - autoplot(Ler_leaf_rflt.spct, annotations = "")) - vdiffr::expect_doppelganger("reflector-minus-annotations-tot", - autoplot(Ler_leaf_rflt.spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("reflector-plus-annotations-tot", - autoplot(Ler_leaf_rflt.spct, annotations = c("+", "boundaries"))) -}) - -test_that("reflector_mspct", { - set_annotations_default() - two_leaves_Rfr.mspct <- reflector_mspct(list(one = Ler_leaf_rflt.spct, - half = Ler_leaf_rflt.spct / 2)) - vdiffr::expect_doppelganger("reflector-mspct-default", - autoplot(two_leaves_Rfr.mspct)) - vdiffr::expect_doppelganger("reflector-mspct-default-range", - autoplot(two_leaves_Rfr.mspct, range = c(500, 700))) - vdiffr::expect_doppelganger("reflector-mspct-no-annotations", - autoplot(two_leaves_Rfr.mspct, annotations = "")) - vdiffr::expect_doppelganger("reflector-mspct-reserve-space", - autoplot(two_leaves_Rfr.mspct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("reflector-mspct-mean", - autoplot(two_leaves_Rfr.mspct, plot.data = "mean")) - vdiffr::expect_doppelganger("reflector-mspct-median", - autoplot(two_leaves_Rfr.mspct, plot.data = "median")) - # triggers warning - # vdiffr::expect_doppelganger("reflector-mspct-sum", - # autoplot(two_leaves_Rfr.mspct, plot.data = "sum")) - testthat::expect_warning(autoplot(two_leaves_Rfr.mspct, plot.data = "sum")) - vdiffr::expect_doppelganger("reflector-mspct-sum", - autoplot(two_leaves_Rfr.mspct, plot.data = "prod")) - vdiffr::expect_doppelganger("reflector-mspct-se", - autoplot(two_leaves_Rfr.mspct, plot.data = "se")) - vdiffr::expect_doppelganger("reflector-mspct-se-ylab", - autoplot(two_leaves_Rfr.mspct, plot.data = "se", ylab = "Standard error of the mean")) - vdiffr::expect_doppelganger("reflector-mspct-var", - autoplot(two_leaves_Rfr.mspct, plot.data = "var")) - vdiffr::expect_doppelganger("reflector-mspct-var-ylab", - autoplot(two_leaves_Rfr.mspct, plot.data = "var", ylab = "Variance")) - vdiffr::expect_doppelganger("reflector-mspct-mean-Tfr", - autoplot(two_leaves_Rfr.mspct, plot.data = "mean", plot.qty = "reflectance")) - vdiffr::expect_doppelganger("reflector-mspct-median-Tfr", - autoplot(two_leaves_Rfr.mspct, plot.data = "median", plot.qty = "reflectance")) -}) - -test_that("object_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("object-default-tot", - autoplot(Ler_leaf.spct)) - vdiffr::expect_doppelganger("object-default-pc-out-tot", - autoplot(Ler_leaf.spct, pc.out = TRUE)) - vdiffr::expect_doppelganger("object-text-size-tot", - autoplot(Ler_leaf.spct, text.size = 3.5)) - vdiffr::expect_doppelganger("object-wb-vis-tot", - autoplot(Ler_leaf.spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("object-range-num-tot", - autoplot(Ler_leaf.spct, range = c(500, 700))) - vdiffr::expect_doppelganger("object-range-wb-tot", - autoplot(Ler_leaf.spct, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("object-no-annotations-tot", - autoplot(Ler_leaf.spct, annotations = "")) - vdiffr::expect_doppelganger("object-reserve-space-tot", - autoplot(Ler_leaf.spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("object-minus-guide-tot", - autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"))) - vdiffr::expect_doppelganger("object-plus-segments-tot", - autoplot(Ler_leaf.spct, annotations = c("+", "segments"))) - - vdiffr::expect_doppelganger("object-default-stk", - autoplot(Ler_leaf.spct, stacked = FALSE)) - vdiffr::expect_doppelganger("object-default-stk-ylim", - autoplot(Ler_leaf.spct, stacked = FALSE, ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("object-default-pc-out-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, pc.out = TRUE)) - vdiffr::expect_doppelganger("object-text-size-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, text.size = 3.5)) - vdiffr::expect_doppelganger("object-minus-peaks-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("-", "peaks"))) - vdiffr::expect_doppelganger("object-peaks-valleys-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("+", "peaks", "valleys"))) - vdiffr::expect_doppelganger("object-plus-valleys-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, span = 401, annotations = c("+", "valleys"))) - vdiffr::expect_doppelganger("object-wb-vis-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, w.band = VIS_bands())) - vdiffr::expect_doppelganger("object-range-num-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, range = c(500, 700))) - vdiffr::expect_doppelganger("object-range-wb-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("object-no-annotations-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, annotations = "")) - vdiffr::expect_doppelganger("object-minus-labels-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, annotations = c("-", "labels"))) - vdiffr::expect_doppelganger("object-plus-segments-stk", - autoplot(Ler_leaf.spct, stacked = FALSE, annotations = c("+", "segments"))) -}) - -test_that("object_spct_as_reflector", { - set_annotations_default() - vdiffr::expect_doppelganger("object-as-reflector-default-tot", - autoplot(Ler_leaf.spct, plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-default-pc-out-tot", - autoplot(Ler_leaf.spct, pc.out = TRUE, plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-text-size-tot", - autoplot(Ler_leaf.spct, text.size = 3.5, plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-wb-vis-tot", - autoplot(Ler_leaf.spct, w.band = VIS_bands(), plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-range-num-tot", - autoplot(Ler_leaf.spct, range = c(500, 700), plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-range-wb-tot", - autoplot(Ler_leaf.spct, range = waveband(c(500, 700)), plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-no-annotations-tot", - autoplot(Ler_leaf.spct, annotations = "", plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-reserve-space-tot", - autoplot(Ler_leaf.spct, annotations = "reserve.space", plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-minus-guide-tot", - autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"), plot.qty = "reflectance")) - vdiffr::expect_doppelganger("object-as-reflector-plus-segments-tot", - autoplot(Ler_leaf.spct, annotations = c("+", "segments"), plot.qty = "reflectance")) -}) - -test_that("object_spct_as_filter", { - set_annotations_default() - vdiffr::expect_doppelganger("object-filter-tfr-default-tot", - autoplot(Ler_leaf.spct, plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-default-pc-out-tot", - autoplot(Ler_leaf.spct, pc.out = TRUE, plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-text-size-tot", - autoplot(Ler_leaf.spct, text.size = 3.5, plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-wb-vis-tot", - autoplot(Ler_leaf.spct, w.band = VIS_bands(), plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-range-num-tot", - autoplot(Ler_leaf.spct, range = c(500, 700), plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-range-wb-tot", - autoplot(Ler_leaf.spct, range = waveband(c(500, 700)), plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-no-annotations-tot", - autoplot(Ler_leaf.spct, annotations = "", plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-reserve-space-tot", - autoplot(Ler_leaf.spct, annotations = "reserve.space", plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-minus-guide-tot", - autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"), plot.qty = "transmittance")) - vdiffr::expect_doppelganger("object-as-filter-tfr-plus-segments-tot", - autoplot(Ler_leaf.spct, annotations = c("+", "segments"), plot.qty = "transmittance")) - - vdiffr::expect_doppelganger("object-as-filter-afr-default-tot", - autoplot(Ler_leaf.spct, plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-default-pc-out-tot", - autoplot(Ler_leaf.spct, pc.out = TRUE, plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-text-size-tot", - autoplot(Ler_leaf.spct, text.size = 3.5, plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-wb-vis-tot", - autoplot(Ler_leaf.spct, w.band = VIS_bands(), plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-range-num-tot", - autoplot(Ler_leaf.spct, range = c(500, 700), plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-range-wb-tot", - autoplot(Ler_leaf.spct, range = waveband(c(500, 700)), plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-no-annotations-tot", - autoplot(Ler_leaf.spct, annotations = "", plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-reserve-space-tot", - autoplot(Ler_leaf.spct, annotations = "reserve.space", plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-minus-guide-tot", - autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"), plot.qty = "absorptance")) - vdiffr::expect_doppelganger("object-as-filter-afr-plus-segments-tot", - autoplot(Ler_leaf.spct, annotations = c("+", "segments"), plot.qty = "absorptance")) - - vdiffr::expect_doppelganger("object-as-filter-a-default-tot", - autoplot(Ler_leaf.spct, plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-default-pc-out-tot", - autoplot(Ler_leaf.spct, pc.out = TRUE, plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-text-size-tot", - autoplot(Ler_leaf.spct, text.size = 3.5, plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-wb-vis-tot", - autoplot(Ler_leaf.spct, w.band = VIS_bands(), plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-range-num-tot", - autoplot(Ler_leaf.spct, range = c(500, 700), plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-range-wb-tot", - autoplot(Ler_leaf.spct, range = waveband(c(500, 700)), plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-no-annotations-tot", - autoplot(Ler_leaf.spct, annotations = "", plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-reserve-space-tot", - autoplot(Ler_leaf.spct, annotations = "reserve.space", plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-minus-guide-tot", - autoplot(Ler_leaf.spct, annotations = c("-", "colour.guide"), plot.qty = "absorbance")) - vdiffr::expect_doppelganger("object-as-filter-a-plus-segments-tot", - autoplot(Ler_leaf.spct, annotations = c("+", "segments"), plot.qty = "absorbance")) -}) - -test_that("response_spct", { - set_annotations_default() - vdiffr::expect_doppelganger("response-default-scaled", - autoplot(fscale(ccd.spct, f = "mean", target = 1))) - vdiffr::expect_doppelganger("response-default-normalized", - autoplot(ccd.spct, norm = 600)) - - vdiffr::expect_doppelganger("response-default", - autoplot(ccd.spct)) - vdiffr::expect_doppelganger("response-default-ylim", - autoplot(ccd.spct, ylim = c(-0.1, 1.2))) - vdiffr::expect_doppelganger("response-text-size", - autoplot(ccd.spct, text.size = 3.5)) - vdiffr::expect_doppelganger("response-span-31", - autoplot(ccd.spct, span = 31)) - vdiffr::expect_doppelganger("response-wb-vis", - autoplot(ccd.spct, w.band = VIS_bands())) - vdiffr::expect_doppelganger("response-label-average", - autoplot(ccd.spct, label.qty = "average")) - vdiffr::expect_doppelganger("response-label-mean", - autoplot(ccd.spct, label.qty = "mean")) - vdiffr::expect_doppelganger("response-label-total", - autoplot(ccd.spct, label.qty = "total")) - vdiffr::expect_doppelganger("response-label-contrib", - autoplot(ccd.spct, label.qty = "contribution")) - vdiffr::expect_doppelganger("response-label-relative", - autoplot(ccd.spct, label.qty = "relative")) - vdiffr::expect_doppelganger("response-range-num", - autoplot(ccd.spct, range = c(300, 700))) - vdiffr::expect_doppelganger("response-range-wb", - autoplot(ccd.spct, range = waveband(c(300, 700)))) - vdiffr::expect_doppelganger("response-no-annotations", - autoplot(ccd.spct, annotations = "")) - vdiffr::expect_doppelganger("response-reserve-space", - autoplot(ccd.spct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("response-minus-annotations", - autoplot(ccd.spct, annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("response-plus-annotations", - autoplot(ccd.spct, annotations = c("+", "boundaries"))) - - vdiffr::expect_doppelganger("response-default-q", - autoplot(ccd.spct, unit.out = "photon")) - vdiffr::expect_doppelganger("response-default-ylim-q", - autoplot(ccd.spct, unit.out = "photon", ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("response-text-size-q", - autoplot(ccd.spct, unit.out = "photon", text.size = 3.5)) - vdiffr::expect_doppelganger("response-span-31-q", - autoplot(ccd.spct, unit.out = "photon", span = 31)) - vdiffr::expect_doppelganger("response-wb-vis-q", - autoplot(ccd.spct, unit.out = "photon", w.band = VIS_bands())) - vdiffr::expect_doppelganger("response-label-average-q", - autoplot(ccd.spct, unit.out = "photon", label.qty = "average")) - vdiffr::expect_doppelganger("response-label-mean-q", - autoplot(ccd.spct, unit.out = "photon", label.qty = "mean")) - vdiffr::expect_doppelganger("response-label-total-q", - autoplot(ccd.spct, unit.out = "photon", label.qty = "total")) - vdiffr::expect_doppelganger("response-label-contrib-q", - autoplot(ccd.spct, unit.out = "photon", label.qty = "contribution")) - vdiffr::expect_doppelganger("response-label-relative-q", - autoplot(ccd.spct, unit.out = "photon", label.qty = "relative")) - vdiffr::expect_doppelganger("response-range-num-q", - autoplot(ccd.spct, unit.out = "photon", range = c(500, 700))) - vdiffr::expect_doppelganger("response-range-wb-q", - autoplot(ccd.spct, unit.out = "photon", range = waveband(c(500, 700)))) - vdiffr::expect_doppelganger("response-no-annotations-q", - autoplot(ccd.spct, unit.out = "photon", annotations = "")) - vdiffr::expect_doppelganger("response-minus-summaries-q", - autoplot(ccd.spct, unit.out = "photon", annotations = c("-", "summaries"))) - vdiffr::expect_doppelganger("response-minus-boxes-q", - autoplot(ccd.spct, unit.out = "photon", annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("response-plus-boundaries-q", - autoplot(ccd.spct, unit.out = "photon", annotations = c("+", "boundaries"))) - vdiffr::expect_doppelganger("response-plus-segments-q", - autoplot(ccd.spct, unit.out = "photon", annotations = c("+", "segments"))) - - # time units - vdiffr::expect_doppelganger("response-second", - autoplot(setTimeUnit(ccd.spct, "second", TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-hour", - autoplot(setTimeUnit(ccd.spct, "hour", TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-day", - autoplot(setTimeUnit(ccd.spct, "day", TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-exposure", - autoplot(setTimeUnit(ccd.spct, "exposure", TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-duration", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(4.5, "minutes"), TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-none", - autoplot(setTimeUnit(ccd.spct, "unknown", TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-seconds", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "seconds"), TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-hours", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "hours"), TRUE), norm = NULL)) - vdiffr::expect_doppelganger("response-days", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "days"), TRUE), norm = NULL)) - - vdiffr::expect_doppelganger("response-second-q", - autoplot(setTimeUnit(ccd.spct, "second", TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-hour-q", - autoplot(setTimeUnit(ccd.spct, "hour", TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-day-q", - autoplot(setTimeUnit(ccd.spct, "day", TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-exposure-q", - autoplot(setTimeUnit(ccd.spct, "exposure", TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-duration-q", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(4.5, "minutes"), TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-none-q", - autoplot(setTimeUnit(ccd.spct, "unknown", TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-seconds-q", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "seconds"), TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-hours-q", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "hours"), TRUE), norm = NULL, unit.out = "photon")) - vdiffr::expect_doppelganger("response-days-q", - autoplot(setTimeUnit(ccd.spct, lubridate::duration(1, "days"), TRUE), norm = NULL, unit.out = "photon")) - - }) - -test_that("response_mspct", { - set_annotations_default() - two_ccds.mspct <- response_mspct(list(one = ccd.spct, - half = ccd.spct / 2)) - - vdiffr::expect_doppelganger("response-mspct-default", - autoplot(two_ccds.mspct)) - vdiffr::expect_doppelganger("response-mspct-default-range", - autoplot(two_ccds.mspct, range = c(500, 700))) - vdiffr::expect_doppelganger("response-mspct-default-e", - autoplot(two_ccds.mspct, unit.out = "energy")) - vdiffr::expect_doppelganger("response-mspct-default-p", - autoplot(two_ccds.mspct, unit.out = "photon")) - vdiffr::expect_doppelganger("response-mspct-no-annotations", - autoplot(two_ccds.mspct, annotations = "")) - vdiffr::expect_doppelganger("response-mspct-reserve-space", - autoplot(two_ccds.mspct, annotations = "reserve.space")) - vdiffr::expect_doppelganger("response-mspct-mean", - autoplot(two_ccds.mspct, plot.data = "mean")) - vdiffr::expect_doppelganger("response-mspct-median", - autoplot(two_ccds.mspct, plot.data = "median")) - vdiffr::expect_doppelganger("response-mspct-sum", - autoplot(two_ccds.mspct, plot.data = "sum")) - # vdiffr::expect_doppelganger("response-mspct-sum", - # autoplot(two_ccds.mspct, plot.data = "prod")) - testthat::expect_warning(autoplot(two_ccds.mspct, plot.data = "prod")) - vdiffr::expect_doppelganger("response-mspct-se", - autoplot(two_ccds.mspct, plot.data = "se")) - vdiffr::expect_doppelganger("response-mspct-se-ylab", - autoplot(two_ccds.mspct, plot.data = "se", ylab = "Standard error of the mean")) - vdiffr::expect_doppelganger("response-mspct-var", - autoplot(two_ccds.mspct, plot.data = "var")) - vdiffr::expect_doppelganger("response-mspct-var-ylab", - autoplot(two_ccds.mspct, plot.data = "var", ylab = "Variance")) - vdiffr::expect_doppelganger("response-mspct-mean-e", - autoplot(two_ccds.mspct, plot.data = "mean", unit.out = "energy")) - vdiffr::expect_doppelganger("response-mspct-mean-p", - autoplot(two_ccds.mspct, plot.data = "mean", unit.out = "photon")) - vdiffr::expect_doppelganger("response-mspct-median-e", - autoplot(two_ccds.mspct, plot.data = "median", unit.out = "energy")) - vdiffr::expect_doppelganger("response-mspct-median-p", - autoplot(two_ccds.mspct, plot.data = "median", unit.out = "photon")) -}) - -test_that("waveband", { - set_annotations_default() - vdiffr::expect_doppelganger("waveband-default-cie", - autoplot(CIE(), range = c(230, 430))) - vdiffr::expect_doppelganger("waveband-default-red", - autoplot(Red())) - vdiffr::expect_doppelganger("waveband-default-ylim", - autoplot(Red(), ylim = c(-0.2, 1.2))) - vdiffr::expect_doppelganger("waveband-text-size", - autoplot(Red(), text.size = 3.5)) - vdiffr::expect_doppelganger("waveband-plus-segments", - autoplot(Red(), annotations = c("+", "segments"))) - vdiffr::expect_doppelganger("waveband-minus-boxes", - autoplot(Red(), annotations = c("-", "boxes"))) - vdiffr::expect_doppelganger("waveband-no-annotations", - autoplot(Red(), annotations = "")) - vdiffr::expect_doppelganger("waveband-reserve-space", - autoplot(Red(), annotations = "reserve.space")) -}) - - -# test_that("plot_spct", { -# set_annotations_default() -# # skip_on_cran() -# vdiffr::expect_doppelganger("raw-default-autop", -# plot(white_led.raw_spct)) -# vdiffr::expect_doppelganger("cps-default-autop", -# plot(white_led.cps_spct)) -# vdiffr::expect_doppelganger("source-default-autop", -# plot(white_led.source_spct)) -# vdiffr::expect_doppelganger("source-product-BSWF-autop", -# plot(sun.spct * CIE())) -# vdiffr::expect_doppelganger("filter-default-tot-autop", -# plot(Ler_leaf_trns.spct)) -# vdiffr::expect_doppelganger("reflector-default-tot-autop", -# plot(Ler_leaf_rflt.spct)) -# vdiffr::expect_doppelganger("object-default-tot-autop", -# plot(Ler_leaf.spct)) -# vdiffr::expect_doppelganger("object-default-stk-autop", -# plot(Ler_leaf.spct, stacked = FALSE)) -# vdiffr::expect_doppelganger("response-default-autop", -# plot(ccd.spct)) -# }) - -test_that("plot_mspct", { - set_annotations_default() - two_ccds.mspct <- response_mspct(list(one = ccd.spct, - half = ccd.spct / 2)) - vdiffr::expect_doppelganger("response-mspct-default-autop", - plot(two_ccds.mspct)) -}) - -test_that("plot_waveband", { - vdiffr::expect_doppelganger("waveband-default-cie-autop", - plot(CIE(), range = c(230, 430))) -}) - -test_that("set_annotations_default", { - set_annotations_default() - expect_null(getOption("photobiology.plot.annotations")) - set_annotations_default("") - expect_setequal(getOption("photobiology.plot.annotations"), "") - set_annotations_default("reserve.space") - expect_setequal(getOption("photobiology.plot.annotations"), "reserve.space") - set_annotations_default() - set_annotations_default(c("+", "title:what:where")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) - set_annotations_default("+") - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) - set_annotations_default("-") - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) - set_annotations_default(c("-", "title")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) - set_annotations_default(c("-", "title*")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("-", "peaks*")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide")) - set_annotations_default(c("+", "peaks")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("+", "peak.labels")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peak.labels")) - set_annotations_default(c("+", "peaks")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("+", "peaks")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("+", "segments")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("segments", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("+", "boxes")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("boxes", "labels", "summaries", "colour.guide", "peaks")) - set_annotations_default(c("=", "segments", "summaries")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("segments", "summaries")) - set_annotations_default(c("=", "")) - expect_setequal(getOption("photobiology.plot.annotations"), "") - set_annotations_default(c("segments", "summaries")) - expect_setequal(getOption("photobiology.plot.annotations"), - c("segments", "summaries")) - set_annotations_default(c("color.guide", "colour.guide")) - expect_setequal(getOption("photobiology.plot.annotations"), "colour.guide") - set_annotations_default() # clean up -}) - -test_that("set_w.band_default", { - set_w.band_default() - expect_null(getOption("photobiology.plot.bands")) - set_w.band_default(UVB()) - expect_setequal(getOption("photobiology.plot.bands"), list(UVB())) - set_w.band_default(UV_bands()) - expect_setequal(getOption("photobiology.plot.bands"), UV_bands()) - expect_warning(set_w.band_default("UVB")) - expect_warning(set_w.band_default(c(400,500))) - expect_warning(set_w.band_default(list(a = 400, b = "a"))) - set_w.band_default() # clean up -}) diff --git a/tests/testthat/test-set-unset-options.R b/tests/testthat/test-set-unset-options.R new file mode 100644 index 00000000..767eb13c --- /dev/null +++ b/tests/testthat/test-set-unset-options.R @@ -0,0 +1,72 @@ +context("set-unset-options") +library(photobiology) + +test_that("set_annotations_default", { + set_annotations_default() + expect_null(getOption("photobiology.plot.annotations")) + set_annotations_default("") + expect_setequal(getOption("photobiology.plot.annotations"), "") + set_annotations_default("reserve.space") + expect_setequal(getOption("photobiology.plot.annotations"), "reserve.space") + set_annotations_default() + set_annotations_default(c("+", "title:what:where")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) + set_annotations_default("+") + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) + set_annotations_default("-") + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) + set_annotations_default(c("-", "title")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks", "title:what:where")) + set_annotations_default(c("-", "title*")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("-", "peaks*")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide")) + set_annotations_default(c("+", "peaks")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("+", "peak.labels")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peak.labels")) + set_annotations_default(c("+", "peaks")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("+", "peaks")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("+", "segments")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("segments", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("+", "boxes")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("boxes", "labels", "summaries", "colour.guide", "peaks")) + set_annotations_default(c("=", "segments", "summaries")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("segments", "summaries")) + set_annotations_default(c("=", "")) + expect_setequal(getOption("photobiology.plot.annotations"), "") + set_annotations_default(c("segments", "summaries")) + expect_setequal(getOption("photobiology.plot.annotations"), + c("segments", "summaries")) + set_annotations_default(c("color.guide", "colour.guide")) + expect_setequal(getOption("photobiology.plot.annotations"), "colour.guide") + set_annotations_default() # clean up +}) + +test_that("set_w.band_default", { + set_w.band_default() + expect_null(getOption("photobiology.plot.bands")) + set_w.band_default(UVB()) + expect_setequal(getOption("photobiology.plot.bands"), list(UVB())) + set_w.band_default(UV_bands()) + expect_setequal(getOption("photobiology.plot.bands"), UV_bands()) + expect_warning(set_w.band_default("UVB")) + expect_warning(set_w.band_default(c(400,500))) + expect_warning(set_w.band_default(list(a = 400, b = "a"))) + set_w.band_default() # clean up +}) diff --git a/vignettes/userguide2-autoplot-methods.R b/vignettes/userguide2-autoplot-methods.R index 5b00d18b..b658df0d 100644 --- a/vignettes/userguide2-autoplot-methods.R +++ b/vignettes/userguide2-autoplot-methods.R @@ -73,7 +73,7 @@ autoplot(sun.spct, w.band = waveband(c(380, 760))) autoplot(sun.spct, w.band = NULL) ## ----eval=FALSE--------------------------------------------------------------- -# set_w.band_default(w.band = Plant_bands()) +# set_w.band_default(w.band = Plant_bands()) ## ----------------------------------------------------------------------------- autoplot(sun_evening.mspct, plot.data = "mean") @@ -164,8 +164,8 @@ autoplot(yellow_gel.spct, plot.qty = "absorbance", wls.target = 2, annotations = list(c("-", "peaks"), c("+", "wls"))) ## ----eval=FALSE, echo=FALSE--------------------------------------------------- -# yellow_gel.spct$Rfr <- 1 - max(yellow_gel.spct$Tfr) -# autoplot(yellow_gel.spct, plot.qty = "absorptance", annotations = c("-", "peaks")) +# yellow_gel.spct$Rfr <- 1 - max(yellow_gel.spct$Tfr) +# autoplot(yellow_gel.spct, plot.qty = "absorptance", annotations = c("-", "peaks")) ## ----------------------------------------------------------------------------- autoplot(sun.spct) + geom_spct(fill = color_of(sun.spct)) + @@ -179,16 +179,16 @@ autoplot(yellow_gel.spct, annotations = c("+", "boundaries")) autoplot(white_led.raw_spct, annotations = c("+", "boundaries")) ## ----eval=FALSE, message = FALSE---------------------------------------------- -# autoplot(white_led.raw_spct[ , c("w.length", "counts_1")], -# annotations = c("+", "boundaries")) +# autoplot(white_led.raw_spct[ , c("w.length", "counts_1")], +# annotations = c("+", "boundaries")) ## ----eval=FALSE--------------------------------------------------------------- -# autoplot(white_led.raw_spct[ , c("w.length", "counts_1", "counts_3")], -# annotations = c("+", "boundaries")) +# autoplot(white_led.raw_spct[ , c("w.length", "counts_1", "counts_3")], +# annotations = c("+", "boundaries")) ## ----eval=FALSE--------------------------------------------------------------- -# # Not run so as to pass CRAN checks!! -# autoplot(yellow_gel.spct - 0.01, annotations = c("+", "boundaries")) +# # Not run so as to pass CRAN checks!! +# autoplot(yellow_gel.spct - 0.01, annotations = c("+", "boundaries")) ## ----------------------------------------------------------------------------- autoplot(sun_evening.mspct, annotations = c("-", "peaks")) + diff --git a/vignettes/userguide2-autoplot-methods.Rmd b/vignettes/userguide2-autoplot-methods.Rmd index c2fbebfb..e7c37ceb 100644 --- a/vignettes/userguide2-autoplot-methods.Rmd +++ b/vignettes/userguide2-autoplot-methods.Rmd @@ -504,6 +504,7 @@ A `autoplot()` method for `waveband` objects is also provided. ```{r} autoplot(VIS()) ``` + ```{r} autoplot(PAR(), range = c(200, 1000), geom = "spct", unit.in = "photon", unit.out = "energy") diff --git a/vignettes/userguide2-autoplot-methods.html b/vignettes/userguide2-autoplot-methods.html index d42faa50..231f0fe7 100644 --- a/vignettes/userguide2-autoplot-methods.html +++ b/vignettes/userguide2-autoplot-methods.html @@ -12,7 +12,7 @@ - + User Guide: 2 Autoplot Methods @@ -62,7 +62,7 @@ } @media print { pre > code.sourceCode { white-space: pre-wrap; } -pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } +pre > code.sourceCode > span { display: inline-block; text-indent: -5em; padding-left: 5em; } } pre.numberSource code { counter-reset: source-line 0; } @@ -339,9 +339,9 @@

User Guide: 2 Autoplot Methods

-

‘ggspectra’ 0.3.12.9001

+

‘ggspectra’ 0.3.14.9000

Pedro J. Aphalo

-

2024-08-02

+

2024-12-23

@@ -398,8 +398,11 @@

Introduction

## Label: sunlight, simulated ## Measured on 2010-06-22 09:51:00 UTC ## Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI -## Time unit 1s -## +## Variables: +## w.length: Wavelength [nm] +## s.e.irrad: Spectral energy irradiance [W m-2 nm-1] +## s.q.irrad: Spectral photon irradiance [mol s-1 m-2 nm-1] +## -- ## w.length s.e.irrad s.q.irrad ## Min. :280.0 Min. :0.0000 Min. :0.000e+00 ## 1st Qu.:409.2 1st Qu.:0.4115 1st Qu.:1.980e-06 @@ -418,8 +421,10 @@

Introduction

## time.04 measured on 2023-06-12 18:41:00.768459 UTC ## time.05 measured on 2023-06-12 18:42:00.769065 UTC ## Measured at 60.227 N, 24.018 E; Viikki, Helsinki, FI -## Time unit 1s -## +## Variables: +## w.length: Wavelength [nm] +## s.e.irrad: Spectral energy irradiance [W m-2 nm-1] +## -- ## w.length s.e.irrad spct.idx ## Min. : 290.0 Min. :0.00000 time.01:1593 ## 1st Qu.: 474.4 1st Qu.:0.02315 time.02:1593 @@ -466,7 +471,7 @@

The basics

The simplest possible call to autoplot() needs only one argument, the object to plot.

autoplot(sun.spct)
-

+

In contrast to the examples in the User Guide 1, here we obtain directly an annotated plot of the solar spectrum at ground level. This would be of limited use without the possibility to adjust the @@ -482,16 +487,16 @@

The basics

spectral values and derived summaries will always use the same base of expression.

autoplot(sun.spct, unit.out = "photon")
-

+

We can build and area + line ("spct") plot instead the default line plot.

autoplot(sun.spct, geom = "spct")
-

+

If a single object contains multiple spectra in long form, they are all plotted. In this case no summary values are displayed as they would overlap.

autoplot(sun_evening.spct)
-

+

In addition to the autoplot() methods for individual spectra and spectra in stored long form (_spct classes), there are autoplot() methods available for collections of @@ -515,21 +520,21 @@

The basics

## [10] "chroma_mspct" "generic_mspct"

The plot using defaults is identical to that above.

autoplot(sun_evening.mspct)
-

+

We can choose a different name for the factor identifying the spectra in the collection.

autoplot(sun_evening.mspct, idfactor = "Spectra")
-

+

With facets, there is only one spectrum per panel. Summaries per waveband are shown.

autoplot(sun_evening.spct, facets = TRUE)
-

+

Above we showed the default faceting by passing facets = TRUE. We can set the number of columns by passing a number. For panels in one column we pass facets = 1, and for two columns we pass facets = 2, and so on.

autoplot(sun_evening.mspct, facets = 2)
-

+

Contrary to "gg" objects created with package ‘ggplot2’, the data embedded in the "gg" objects created with these @@ -562,11 +567,35 @@

The basics

## position_identity ## ## geom_text: na.rm = TRUE -## stat_peaks: span = NULL, ignore_threshold = 0.02, strict = TRUE, refine.wl = FALSE, method = spline, chroma.type = CMF, label.fmt = %.4g, x.label.fmt = %.4g, y.label.fmt = %.4g, na.rm = TRUE +## stat_peaks: span = NULL, ignore_threshold = 0.02, strict = TRUE, refine.wl = FALSE, method = spline, chroma.type = CMF, label.fmt = %.4g, x.label.fmt = %.4g, y.label.fmt = %.4g, x.label.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, y.label.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, x.colour.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, na.rm = TRUE ## position_nudge ## ## geom_point: na.rm = TRUE -## stat_peaks: span = NULL, ignore_threshold = 0.02, strict = TRUE, refine.wl = FALSE, method = spline, chroma.type = CMF, label.fmt = %.3g, x.label.fmt = %.3g, y.label.fmt = %.3g, na.rm = TRUE +## stat_peaks: span = NULL, ignore_threshold = 0.02, strict = TRUE, refine.wl = FALSE, method = spline, chroma.type = CMF, label.fmt = %.3g, x.label.fmt = %.3g, y.label.fmt = %.3g, x.label.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, y.label.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, x.colour.transform = function (x) +## { +## class(x) <- unique.default(c("AsIs", oldClass(x))) +## x +## }, na.rm = TRUE ## position_identity ## ## geom_rect: na.rm = TRUE @@ -594,8 +623,10 @@

The basics

## Label: sunlight, simulated ## Measured on 2010-06-22 09:51:00 UTC ## Measured at 60.20911 N, 24.96474 E; Kumpula, Helsinki, FI -## Time unit 1s -## +## Variables: +## w.length: Wavelength [nm] +## s.e.irrad: Spectral energy irradiance [W m-2 nm-1] +## -- ## w.length s.e.irrad ## Min. :280.0 Min. :0.0000 ## 1st Qu.:409.2 1st Qu.:0.4115 @@ -616,22 +647,22 @@

Wavelengths

classes, such as class source_spct, or a waveband definition.

autoplot(sun.spct, range = c(400, 700))
-

+

We can show summaries for different wavebands, by passing them to parameter w.band. We can pass either individual wavebands or lists of wavebands. First a list of wavebands created with a constructor, here showing the limits based on the ISO standard.

autoplot(sun.spct, w.band = photobiologyWavebands::VIS_bands("ISO"))
-

+

A single waveband can also be created with a generic constructor.

autoplot(sun.spct, w.band = waveband(c(380, 760)))
-

+

NULL as argument for w.band is replaced by a waveband covering the full range of the spectral data. The whole range is the range plotted, which is controlled by the argument passed to range.

autoplot(sun.spct, w.band = NULL)
-

+

Summarizing the examples above, arguments passed to range and w.band play very different roles. Parameter range, gives the wavelengths to include in the @@ -666,7 +697,7 @@

“Parallel” summaries

spectra. Currently implemented only for spectra with identical wavelength vectors and of the same class.

autoplot(sun_evening.mspct, plot.data = "mean")
-

+

Summary quantities by waveband

@@ -680,7 +711,7 @@

Summary quantities by waveband

labels. Note that the units and quantity labels for the waveband summaries have also changed.

autoplot(sun.spct, label.qty = "mean")
-

+

Two label.qty values need explanation. The first one, "relative" displays in labels the relative contribution of the integral of each waveband, to the sum of the integrals of all @@ -697,10 +728,10 @@

Summary quantities by waveband

wavebands cover the whole range of wavelengths in the spectrum, the sum of the summary values is less than 100.

autoplot(sun.spct, label.qty = "contribution.pc")
-

+

When using "relative.pc" the sum adds to 100.

autoplot(sun.spct, label.qty = "relative.pc")
-

+

Automatic annotations

@@ -900,42 +931,42 @@

Automatic annotations

We add a title, subtitle and caption.

autoplot(sun.spct, 
      annotations = c("+", "title:objt:when:where"))
-

+

We use “none” as a filler so that only subtitle and caption are added to the plot.

autoplot(sun.spct, 
      annotations = c("+", "title:none:what:where"))
-

+

With "boundaries", we add one or two horizontal dashed lines showing the valid range of values. It does not override any other annotation. (The boundary line is shown in red when a plot displays out-of-range spectral data.)

autoplot(sun.spct, 
      annotations = c("+", "boundaries"))
-

+

We can list all the annotations to be included in a plot, in which case "=" is optional so as to maintain compatibility with earlier versions.

autoplot(sun.spct, 
      annotations = c("=", "labels", "summaries", "color.guide", "peaks", "boundaries"))
-

+

As indicated in the table above, some annotations override other annotations which fulfill a similar role. Here "segments" overrides the "boxes", included in the default annotations.

autoplot(sun.spct, 
      annotations = c("+", "segments"))
-

+

We can also remove some of the default annotations on a case by case basis.

autoplot(sun.spct, annotations = c("-", "summaries", "peaks"))
-

+

The behaviour of some annotations can be tweaked. Below we add "valleys" as annotations, and control with span how close to each other are the peaks and valleys found.

autoplot(sun.spct, annotations = c("+", "valleys"), span = 41)
-

+

The annotations "peak.labels" and "valley.labels" override "peaks" and "valleys". They use the repulsive geometry @@ -944,29 +975,29 @@

Automatic annotations

annotations = list(c("+", "peak.labels"), c("-", "boxes", "summaries", "labels")), span = 21)
-

+

autoplot(sun.spct, 
          annotations = list(c("+", "valley.labels"), 
                             c("-", "peaks")), 
          span = 31)
-

+

autoplot(sun.spct, annotations = c("+", "peak.labels", "valley.labels"), span = 31)
-

+

Passing "" as argument to annotations results in a plot with no annotations, and no extra expansion of scale limits.

autoplot(sun.spct, annotations = "")
-

+

Passing "reserve.space" as argument to annotations results in a plot with no annotations, but with scale limits expanded so as to receive annotations.

autoplot(sun.spct, annotations = "reserve.space")
-

+

The size of the font used for the annotations is controlled by argument text.size.

autoplot(sun.spct, annotations = c("=", "segments", "labels", "color.guide"), 
      text.size = 3.5)
-

+

Argument ylim allows to manually set the limits of the \(y\) axis using the same syntax as in package ‘ggplot2’. The annotations are still automatically positioned, @@ -974,7 +1005,7 @@

Automatic annotations

passed to ylim still give the “space” available for plotting data.

autoplot(sun.spct, ylim = c(NA, 1))
-

+

The time base of the spectral unit or the duration of the exposure is stored as metadata. As demonstrated here using spectral data integrated over 24 h, a one-day-long exposure, the units in the axis labels change @@ -982,7 +1013,7 @@

Automatic annotations

getTimeUnit(sun.daily.spct)
## [1] "day"
autoplot(sun.daily.spct)
-

+

Even though the autoplot() methods can return a finished plot, the returned object is a ggplot object and can be built upon by adding additional elements like facets, @@ -991,7 +1022,7 @@

Automatic annotations

linetype.

autoplot(sun_evening.spct, facets = 3) +
   geom_vline(xintercept = c(400, 700), linetype = "dashed")
-

+

It is possible to construct and bind the spectra on-the-fly, and to use arbitrary variable names for the index factor. This works automatically as long as row binding is done with function @@ -1000,7 +1031,7 @@

Automatic annotations

rbindspct(list(sun = sun.spct, filtered = yellow_gel.spct * sun.spct), idfactor = "Source") autoplot(filter_no_yes.spct) -

+

In the examples above the source_spct object sun.spct was used. The autoplot() methods for other spectral classes have only slight differences. We show some @@ -1009,14 +1040,14 @@

Automatic annotations

valleys.

autoplot(yellow_gel.spct, 
          annotations = list(c("-", "peaks"), c("+", "wls")))
-

+

In many cases it is possible to convert on-the-fly the quantity plotted. In this case, given that the data are clipped as absorbance, a fixed target of A = 2 for the cut-off to be labelled with the wavelength is appropriate.

autoplot(yellow_gel.spct, plot.qty = "absorbance", wls.target = 2,
          annotations = list(c("-", "peaks"), c("+", "wls")))
-

+

If one needs to, one can add a suitable layer function, geom or stat, using ‘local’ data, as shown here, or plot default @@ -1024,13 +1055,13 @@

Automatic annotations

autoplot(sun.spct) + geom_spct(fill = color_of(sun.spct)) + 
   geom_spct(data = yellow_gel.spct * sun.spct, color = "black", 
             fill = color_of(yellow_gel.spct * sun.spct))
-

+

In the case of quantities like transmittance which have a certain range of valid values, both upper and lower boundaries are highlighted, but in other cases only one, or even none depending on the possible valid ranges for the spectral quantities.

autoplot(yellow_gel.spct, annotations = c("+", "boundaries"))
-

+

Differently from other classes raw_spct and cps_spct objects can contain multiple columns of data, normally measured different integartion times, and meant to be combined @@ -1039,7 +1070,7 @@

Automatic annotations

descriptor as metadata, the upper boundary is set to the maximum counts of the detector.

autoplot(white_led.raw_spct, annotations = c("+", "boundaries"))
-

+

Both raw_spct and cps_spct objects contain multiple data columns when integration time bracketing has been used during data acquisition. In such cases, if one wants to plot only one of @@ -1072,7 +1103,7 @@

Editing plots and adding layers

autoplot(sun_evening.mspct, annotations = c("-", "peaks")) +
   aes(color = ifelse(spct.idx == "time.05", "black", "darkred")) +
   theme(legend.position = "none")
-

+

Plots created with autoplot() methods are ggplot objects and can be customized, bearing in mind that any added layers will be plotted on top or existing layers (that is @@ -1088,21 +1119,21 @@

Editing plots and adding layers

label.fmt = "max at %3.1f nm", vjust = -0.5, hjust = 0, color = "red", size = 3) -

+

Ploting wavebands

A autoplot() method for waveband objects is also provided.

autoplot(VIS())
-

+

autoplot(PAR(), range = c(200, 1000), geom = "spct", 
          unit.in = "photon", unit.out = "energy")
-

+

autoplot(CIE(), range = CIE(), annotations = c("-", "color.guide"))
-

+

autoplot(DNA_N(), range = c(270, 420), annotations = c("-", "color.guide"))
-

+