Merge branch 'v0.4.0-photobioloy-v0.12.0'

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),

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

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,

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)
@@ -370,24 +358,16 @@ 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,
                                       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,
-                                        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,