Merge pull request #11 from aphalo/develop-0.3.13

Update autoplot() methods
aphalo · Jul 6, 2024 · a413893 · a413893
2 parents efee4af + a257689
commit a413893
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: ggspectra
 Type: Package
 Title: Extensions to 'ggplot2' for Radiation Spectra
-Version: 0.3.12.9000
-Date: 2024-04-26
+Version: 0.3.12.9001
+Date: 2024-07-06
 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 (> 0.11.1),
+    photobiology (>= 0.11.2),
     ggplot2 (>= 3.4.0)
 Imports:
     photobiologyWavebands (>= 0.5.1),
@@ -36,5 +36,5 @@ URL: https://docs.r4photobiology.info/ggspectra/,
     https://github.com/aphalo/ggspectra/
 BugReports: https://github.com/aphalo/ggspectra/issues/
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/NEWS.md b/NEWS.md
@@ -19,11 +19,18 @@ to avoid "surprising" users.
 formal parameter `add.symbols` with default given by R option 
 `ggspectra.add.symbols`.
 - Revise _scales_ for transmittance, absorptance and reflectance and the 
-matching _axis-label building functions_ by adding
-formal parameter `pc.out` with default given by R option 
-`ggspectra.pc.out`.
-- Revise all autoplot methods so that the default for their `pc.out` defaults
+matching _axis-label building functions_ by adding formal parameter `pc.out` 
+with default given by R option `ggspectra.pc.out`.
+- Revise all `autoplot()` methods so that the default for their `pc.out` defaults
 to the value of R option `ggspectra.pc.out`.
+- Revise all `autoplot()` methods  for objects of class `generic_spct` and 
+derived so that summaries requested by arguments passed to parameter `plot.data`
+are computed for multiple spectra in long form like they were for collections
+of spectra.
+- Fix broken `idfactor` handling in `autoplot()` methods for objects of class `generic_spct` and derived.
+- Use in `autoplot()` methods a plotmath expression for the wavelength axis 
+label, including lambda as symbol, for consistency with the labels of the 
+_y_-axis.
 
 # ggspectra 0.3.12
 

diff --git a/R/autoplot-calibration-spct.R b/R/autoplot-calibration-spct.R
@@ -193,7 +193,7 @@ cal_plot <- function(spct,
     plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2)
   }
   plot <- plot + geom_line(na.rm = na.rm)
-  plot <- plot + labs(x = "Wavelength (nm)", y = s.counts.label)
+  plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.counts.label)
 
   if (length(annotations) == 1 && annotations == "") {
     return(plot)
@@ -230,68 +230,18 @@ cal_plot <- function(spct,
 
 }
 
-#' Create a complete ggplot for an irradiation calibration spectrum.
+#' Plot one or more irradiance-calibration spectra.
 #'
-#' These methods return a ggplot object with an annotated plot of a
-#' calibration_spct object or of the spectra contained in a calibration_mspct
+#' These methods return a ggplot object with an annotated plot of the spectral
+#' data contained in a \code{calibration_spct} or a \code{calibration_mspct}
 #' object.
 #'
-#' @note Note that scales are expanded so as to make space for the annotations.
-#' The object returned is a ggplot object, and can be further manipulated.
-#'
 #' @inheritSection decoration Plot Annotations
 #' @inheritSection autotitle Title Annotations
+#' @inherit autoplot.source_spct
 #'
 #' @param object a calibration_spct object or a calibration_mspct object.
-#' @param ... in the case of collections of spectra, additional arguments passed
-#'   to the plot methods for individual spectra, otherwise currently ignored.
-#' @param w.band a single waveband object or a list of waveband objects.
-#' @param range an R object on which range() returns a vector of length 2, with
-#'   min annd max wavelengths (nm).
-#' @param norm numeric Normalization wavelength (nm) or character string "max",
-#'   or "min" for normalization at the corresponding wavelength, "update" to
-#'   update the normalization after modifying units of expression, quantity
-#'   or range but respecting the previously used criterion, or "skip" to force
-#'   return of \code{object} unchanged. Always skipped for
-#'   \code{plot.qty == "all"}, which is the default.
 #' @param unit.out character IGNORED.
-#' @param pc.out logical, if TRUE use percents instead of fraction of one.
-#' @param label.qty character string giving the type of summary quantity to use
-#'   for labels, one of "mean", "total", "contribution", and "relative".
-#' @param span a peak is defined as an element in a sequence which is greater
-#'   than all other elements within a window of width span centered at that
-#'   element.
-#' @param wls.target numeric vector indicating the spectral quantity values for
-#'   which wavelengths are to be searched and interpolated if need. The
-#'   \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 annotations a character vector ("summaries" is ignored). For details
-#'   please see sections Plot Annotations and Title Annotations.
-#' @param geom character The name of a ggplot geometry, currently only
-#'   \code{"area"}, \code{"spct"} and \code{"line"}. The default \code{NULL}
-#'   selects between them based on \code{stacked}.
-#' @param time.format character Format as accepted by
-#'   \code{\link[base]{strptime}}.
-#' @param tz character Time zone to use for title and/or subtitle.
-#' @param norm numeric normalization wavelength (nm) or character string "max"
-#'   for normalization at the wavelength of highest peak.
-#' @param text.size numeric size of text in the plot decorations.
-#' @param idfactor character Name of an index column in data holding a
-#'   \code{factor} with each spectrum in a long-form multispectrum object
-#'   corresponding to a distinct spectrum. If \code{idfactor=NULL} the name of
-#'   the factor is retrieved from metadata or if no metadata found, the default
-#'   "spct.idx" is tried. If \code{idfactor=NA} no aesthetic is mapped to the
-#'   spectra and the user needs to use 'ggplot2' functions to manually map an
-#'   aesthetic or use facets for the spectra.
-#' @param facets logical or integer Indicating if facets are to be created for
-#'   the levels of \code{idfactor} when \code{spct} contain multiple spectra in
-#'   long form.
-#' @param ylim numeric y axis limits,
-#' @param object.label character The name of the object being plotted.
-#' @param na.rm logical.
-#'
-#' @return a \code{ggplot} object.
 #'
 #' @seealso \code{\link[photobiology]{normalize}},
 #'   \code{\link[photobiology]{calibration_spct}},
@@ -321,10 +271,44 @@ autoplot.calibration_spct <-
            text.size = 2.5,
            idfactor = NULL,
            facets = FALSE,
+           plot.data = "as.is",
            ylim = c(NA, NA),
            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
+    }
+
+    if (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)
+      )
+    }
+
     force(object.label)
 
     annotations.default <-
@@ -367,11 +351,6 @@ autoplot.calibration_spct <-
 
 #' @rdname autoplot.calibration_spct
 #'
-#' @param plot.data character Data to plot. Default is "as.is" plotting one line
-#'   per spectrum. When passing "mean", "median", "sum", "prod", var", "sd",
-#'   "se" as argument all the spectra must contain data at the same wavelength
-#'   values.
-#'
 #' @export
 #'
 autoplot.calibration_mspct <-

diff --git a/R/autoplot-cps-spct.r b/R/autoplot-cps-spct.r
@@ -164,7 +164,7 @@ cps_plot <- function(spct,
     plot <- plot + geom_spct(fill = "black", colour = NA, alpha = 0.2)
   }
   plot <- plot + geom_line(na.rm = na.rm)
-  plot <- plot + labs(x = "Wavelength (nm)", y = s.cps.label)
+  plot <- plot + labs(x = expression("Wavelength, "*lambda~(nm)), y = s.cps.label)
 
   if (length(annotations) == 1 && annotations == "") {
     return(plot)
@@ -214,60 +214,17 @@ cps_plot <- function(spct,
 
 }
 
-#' Create a complete ggplot for detector-counts per second spectra.
+#' Plot one or more detector-counts-per-second spectra.
 #'
-#' This function returns a ggplot object with an annotated plot of a
-#' response_spct object.
-#'
-#' Note that scales are expanded so as to make space for the annotations. The
-#' object returned is a ggplot objects, and can be further manipulated.
+#' These methods return a ggplot object with an annotated plot of a
+#' \code{cps_spct} or a \code{cps_mspct} object.
 #'
 #' @inheritSection decoration Plot Annotations
 #' @inheritSection autotitle Title Annotations
+#' @inherit autoplot.source_spct
 #'
 #' @param object a cps_spct object.
-#' @param ... in the case of collections of spectra, additional arguments passed
-#'   to the plot methods for individual spectra, otherwise currently ignored.
-#' @param w.band a single waveband object or a list of waveband objects.
-#' @param range an R object on which range() returns a vector of length 2, with
-#'   min annd max wavelengths (nm).
 #' @param unit.out character IGNORED.
-#' @param pc.out logical, if TRUE use percent instead of fraction of one for
-#'   normalized spectral data.
-#' @param label.qty character string giving the type of summary quantity to use
-#'   for labels, one of "mean", "total", "contribution", and "relative".
-#' @param span a peak is defined as an element in a sequence which is greater
-#'   than all other elements within a window of width span centered at that
-#'   element.
-#' @param wls.target numeric vector indicating the spectral quantity values for
-#'   which wavelengths are to be searched and interpolated if need. The
-#'   \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 annotations a character vector ("summaries" is ignored). For details
-#'   please see sections Plot Annotations and Title Annotations.
-#' @param geom character The name of a ggplot geometry, currently only
-#'   \code{"area"}, \code{"spct"} and \code{"line"}. The default \code{NULL}
-#'   selects between them based on \code{stacked}.
-#' @param time.format character Format as accepted by \code{\link[base]{strptime}}.
-#' @param tz character Time zone to use for title and/or subtitle.
-#' @param norm numeric normalization wavelength (nm) or character string
-#'   \code{"max"} for normalization at the wavelength of highest peak or
-#'   \code{"skip"} for no change to exisitng normalization in \code{object}.
-#' @param text.size numeric size of text in the plot decorations.
-#' @param idfactor character Name of an index column in data holding a
-#'   \code{factor} with each spectrum in a long-form multispectrum object
-#'   corresponding to a distinct spectrum. If \code{idfactor=NULL} the name of
-#'   the factor is retrieved from metadata or if no metadata found, the
-#'   default "spct.idx" is tried.
-#' @param facets logical or integer Indicating if facets are to be created for
-#'   the levels of \code{idfactor} when \code{spct} contain multiple spectra in
-#'   long form.
-#' @param ylim numeric y axis limits,
-#' @param object.label character The name of the object being plotted.
-#' @param na.rm logical.
-#'
-#' @return a \code{ggplot} object.
 #'
 #' @seealso \code{\link[photobiology]{normalize}},
 #'   \code{\link[photobiology]{cps_spct}},
@@ -311,10 +268,44 @@ autoplot.cps_spct <-
            text.size = 2.5,
            idfactor = NULL,
            facets = FALSE,
+           plot.data = "as.is",
            ylim = c(NA, NA),
            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
+    }
+
+    if (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)
+      )
+    }
+
     force(object.label)
 
     annotations.default <-
@@ -367,11 +358,6 @@ autoplot.cps_spct <-
 
 #' @rdname autoplot.cps_spct
 #'
-#' @param plot.data character Data to plot. Default is "as.is" plotting one line
-#'   per spectrum. When passing "mean", "median", "sum", "prod", "var", "sd",
-#'   "se" as argument all the spectra must contain data at the same wavelength
-#'   values.
-#'
 #' @export
 #'
 autoplot.cps_mspct <-