Minor edits

Handle edge case of idfactor = "" gracefully.
Edit docs and vignette.

R/autoplot-source-spct.r

@@ -633,9 +633,10 @@ q_plot <- function(spct,
 #' @param chroma.type character one of \code{"CMF"} (color matching function) or
 #'   \code{"CC"} (color coordinates) or a
 #'   \code{\link[photobiology]{chroma_spct}} object.
-#' @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 level of the factor.
+#' @param idfactor character Name of an index \code{factor} used to identify
+#'   each spectrum when multiple spectra are included in a plot. If different
+#'   from an existing one, renaming takes place. It is used as title for the
+#'   plot guide and may include embedded spaces and new lines.
 #' @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.
@@ -662,11 +663,11 @@ q_plot <- function(spct,
 #'   different classes for storage of spectral data defined in package
 #'   \code{\link[photobiology]{photobiology}}.
 #'
-#' @note  If \code{idfactor = NULL}, the default for single spectra, the name of
-#'   the factor is retrieved from metadata or if no metadata found, the default
-#'   \code{"spct.idx"} is tried. The default for multiple spectra is to create a
-#'   factor named \code{"spct.idx"}, but if a different name is passed, it will
-#'   be used instead, possibly renaming a pre-existing one.
+#' @note If \code{idfactor = NULL}, the default, the name of the factor is
+#'   retrieved from metadata or if no metadata found, the default
+#'   \code{"spct.idx"} is tried. The default for collections of spectra is to
+#'   create a factor named \code{"spct.idx"}, but if a different name is passed,
+#'   it will be used instead, possibly renaming a pre-existing one.
 #'
 #' @return A \code{ggplot} object with a number of layers that depends on the
 #'   data and annotations.

R/utils-internal.R

@@ -14,7 +14,7 @@ check_idfactor_arg <- function(object, idfactor = NULL, default = FALSE) {
     idfactor <- idfactor[1]
   }
   if (is.null(idfactor) || is.na(idfactor)) {
-    idfactor <- photobiology::getIdFactor(object)
+    idfactor <- photobiology::getIdFactor(object) # may return NA!
   }
   if (is.na(idfactor) || !is.character(idfactor)) {
     idfactor <- default || photobiology::getMultipleWl(object) > 1L
@@ -24,21 +24,26 @@ check_idfactor_arg <- function(object, idfactor = NULL, default = FALSE) {
 
 #' Update idfactor name in object
 #'
+#' Conditionally call \code{\link[photobiology]{setIdFactor}}.
+#'
 #' @param object generic_spct object.
 #' @param idfactor character The name of the factor identifying spectra when
 #'   stored in long form.
 #'
+#' @note There is no check for \code{NA} or \code{NULL} as we assume that
+#'   \code{\link{check_idfactor_arg}} has already been called on \code{idfactor}
+#'   to check its sanity.
+#'
 #' @keywords internal
 #'
 rename_idfactor <- function(object, idfactor) {
-  if (is.character(idfactor) &&
+  if (is.character(idfactor) && nzchar(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
@@ -62,7 +67,7 @@ duration2character <- function(time.unit) {
 #' @keywords internal
 #'
 warn_norm_arg <- function(norm) {
-  if (!is.na(norm)) {
+  if (is.null(norm) || !is.na(norm)) {
     warning("On-the-fly normalization no longer supported. Use 'normalize()' instead.")
   }
 }

vignettes/userguide2-autoplot-methods.R

@@ -57,7 +57,6 @@ autoplot(sun_evening.mspct, facets = 2)
 
 ## -----------------------------------------------------------------------------
 p1 <- autoplot(sun.spct)
-summary(p1)
 summary(p1$data)
 
 ## -----------------------------------------------------------------------------
@@ -152,7 +151,7 @@ autoplot(sun_evening.spct, facets = 3) +
 ## -----------------------------------------------------------------------------
 filter_no_yes.spct <- 
   rbindspct(list(sun = sun.spct, filtered = yellow_gel.spct * sun.spct), 
-            idfactor = "Source")
+            idfactor = "Light source")
 autoplot(filter_no_yes.spct)
 
 ## -----------------------------------------------------------------------------

vignettes/userguide2-autoplot-methods.Rmd

@@ -158,11 +158,10 @@ Contrary to `"gg"` objects created with package 'ggplot2', the data embedded in
 
 ```{r}
 p1 <- autoplot(sun.spct)
-summary(p1)
 summary(p1$data)
 ```
 
-This makes it possible to trace the origin of the data, and also to apply especialised methods to them.
+This makes it possible to trace the origin of the data, and also to apply specialised methods to them.
 
 ---
 
@@ -202,7 +201,7 @@ The effect of `range` is slightly different to the effect of `ggplot2::xlim()` a
 
 ---
 
-The default argument to `parameter `w.band` can be changed by setting 
+The default argument to parameter `w.band` can be changed by setting 
 the R option `"photobiology.plot.bands"` to a single waveband object or to a list waveband
 objects.
 
@@ -407,7 +406,7 @@ It is possible to construct and bind the spectra on-the-fly, and to use arbitrar
 ```{r}
 filter_no_yes.spct <- 
   rbindspct(list(sun = sun.spct, filtered = yellow_gel.spct * sun.spct), 
-            idfactor = "Source")
+            idfactor = "Light source")
 autoplot(filter_no_yes.spct)
 ```