Cleanup remaining norm = .... from autoplot() calls

Also update NEWS and run benchmarks. Delete benchmarks raw data as the files are huge.

NEWS.md

@@ -8,9 +8,14 @@ editor_options:
 
 - 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.
+normalization is updated when the unit or quantity is modified for plotting.
 - 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.
+long form can now be used to rename the existing `idfactor` of the spectral
+object for plotted.
+- The y-scale functions now accept other than numeric values as arguments to
+parameter `normalized`, character values are used as is as subscript, typically
+for the type normalization. In case of logical `TRUE`, `"norm"` is used as
+subindex.
 
 # ggspectra 0.3.15
 

R/autoplot-calibration-spct.R

@@ -288,7 +288,6 @@ autoplot.calibration_spct <-
         autoplot(object = subset2mspct(object),
                  w.band = w.band,
                  range = range,
-                 norm = norm,
                  unit.out = unit.out,
                  pc.out = pc.out,
                  label.qty = label.qty,
@@ -333,7 +332,7 @@ autoplot.calibration_spct <-
              pc.out = pc.out,
              annotations = annotations,
              geom = geom,
-             norm = norm,
+             norm = FALSE, # cal_plot needs to be updated
              text.size = text.size,
              idfactor = idfactor,
              facets = facets,
@@ -388,7 +387,6 @@ autoplot.calibration_mspct <-
       autoplot(object = z,
                range = getOption("ggspectra.wlrange", default = NULL),
                unit.out = unit.out,
-               norm = norm,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
                facets = facets,
@@ -401,7 +399,6 @@ autoplot.calibration_mspct <-
                y.name = paste("irrad.mult", plot.data, sep = "."),
                range = getOption("ggspectra.wlrange", default = NULL),
                unit.out = unit.out,
-               norm = norm,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
                facets = facets,

R/autoplot-cps-spct.r

@@ -236,7 +236,7 @@ cps_plot <- function(spct,
 #'
 #' autoplot(white_led.cps_spct)
 #' autoplot(white_led.cps_spct, geom = "spct")
-#' autoplot(white_led.cps_spct, norm = "max")
+#' autoplot(normalize(white_led.cps_spct, norm = "max"))
 #'
 #' two_leds.mspct <-
 #'   cps_mspct(list("LED 1" = white_led.cps_spct,
@@ -281,7 +281,6 @@ autoplot.cps_spct <-
         autoplot(object = subset2mspct(object),
                  w.band = w.band,
                  range = range,
-                 norm = norm,
                  unit.out = unit.out,
                  pc.out = pc.out,
                  label.qty = label.qty,
@@ -348,7 +347,7 @@ autoplot.cps_mspct <-
   function(object,
            ...,
            range = getOption("ggspectra.wlrange", default = NULL),
-           norm = "skip",
+           norm = NA,
            unit.out = NULL,
            pc.out = getOption("ggspectra.pc.out", default = FALSE),
            idfactor = TRUE,
@@ -383,7 +382,6 @@ autoplot.cps_mspct <-
     if (is.cps_spct(z) && any(c("cps", "cps_1") %in% names(z))) {
       autoplot(object = z,
                range = getOption("ggspectra.wlrange", default = NULL),
-               norm = norm,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
                facets = facets,
@@ -395,7 +393,6 @@ autoplot.cps_mspct <-
       autoplot(object = z,
                y.name = paste("cps", plot.data, sep = "."),
                range = getOption("ggspectra.wlrange", default = NULL),
-               norm = norm,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
                facets = facets,

R/autoplot-raw-spct.r

@@ -414,7 +414,6 @@ autoplot.raw_mspct <-
     if (is.raw_spct(z) && any(c("counts", "counts_1") %in% names(z))) {
       autoplot(object = z,
                range = getOption("ggspectra.wlrange", default = NULL),
-               norm = norm,
                unit.out = unit.out,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
@@ -427,7 +426,6 @@ autoplot.raw_mspct <-
       autoplot(object = z,
                y.name = paste("counts", plot.data, sep = "."),
                range = getOption("ggspectra.wlrange", default = NULL),
-               norm = norm,
                pc.out = pc.out,
                idfactor = NULL, # use idfactor already set in z
                facets = facets,

R/autoplot-response-spct.r

@@ -583,7 +583,6 @@ autoplot.response_spct <-
         autoplot(object = photobiology::subset2mspct(object),
                  w.band = w.band,
                  range = range,
-                 norm = norm,
                  pc.out = pc.out,
                  label.qty = label.qty,
                  span = span,
@@ -735,7 +734,6 @@ autoplot.response_mspct <-
     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,
@@ -748,7 +746,6 @@ autoplot.response_mspct <-
       autoplot(object = z,
                y.name = paste(col.name[unit.out], plot.data, sep = "."),
                range = NULL,
-               norm = norm,
                pc.out = pc.out,
                facets = facets,
                idfactor = NULL, # use idfactor already set in z

inst-not/benchmark-autoplot.R

@@ -60,7 +60,7 @@ p10 <- autoplot(sun_evening.spct)
 p11 <- autoplot(sun_evening.mspct)
 p12 <- autoplot(sun_evening.spct, annotations = "")
 p13 <- autoplot(sun_evening.mspct, annotations = "")
-p14 <- autoplot(sun_evening.mspct, annotations = "", norm = "skip")
+p14 <- autoplot(sun_evening.mspct, annotations = "", idfactor = "Times")
 p15 <- autoplot(sun_evening.spct, facets = 2)
 p16 <- autoplot(sun_evening.mspct, facets = 2)
 p17 <- autoplot(sun_evening.spct, plot.data = "mean")