Fix graphical parameters (again)

R/AllGenerics.R

@@ -560,38 +560,40 @@ NULL
 #' @param sup A [`logical`] scalar: should the supplementary observations be
 #'  plotted?
 #' @param labels A [`logical`] scalar: should labels be drawn?
-#' @param map_color,map_shape,map_size A vector specifying the
-#'  information to be highlighted. It will be mapped to the corresponding
-#'  aesthetic (see examples and vignettes).
+#' @param highlight A vector specifying the information to be highlighted.
+#'  If `NULL` (the default), no highlighting is applied.
+#'  It will only be mapped if at least one [graphical parameters][graphics::par]
+#'  is explicitly specified (see examples).
 #'  If a single `character` string is passed, it must be one of "`observation`",
-#'  "`mass`", "`sum`", "`contribution`" or "`cos2`" (see details).
+#'  "`mass`", "`sum`", "`contribution`" or "`cos2`" (see [`augment()`]).
 #'  Any unambiguous substring can be given.
-#'  If `NULL` (the default), no highlighting is applied.
 #' @param main A [`character`] string giving a main title for the plot.
 #' @param sub A [`character`] string giving a subtitle for the plot.
+#' @param panel.first An an `expression` to be evaluated after the plot axes are
+#'  set up but before any plotting takes place. This can be useful for drawing
+#'  background grids.
+#' @param panel.last An `expression` to be evaluated after plotting has taken
+#'  place but before the axes, title and box are added.
 #' @param ... Further [graphical parameters][graphics::par] (see details).
 #' @details
-#'  Available statistics:
-#'  \describe{
-#'   \item{`observation`}{Whether an observation is active or supplementary.}
-#'   \item{`mass`}{Weight/mass of each observation.}
-#'   \item{`sum`}{Sum of squared coordinates along `axes`.}
-#'   \item{`contribution`}{Joint contributions to the definition of `axes`.}
-#'   \item{`cos2`}{Joint \eqn{cos^2}{cos2} along `axes`.}
-#'  }
-#'
 #'  Commonly used [graphical parameters][graphics::par] are:
 #'  \describe{
-#'   \item{`col`}{The colors for lines and points. Multiple colors can be
-#'                specified so that each point can be given its own color.}
-#'   \item{`pch`}{A vector of plotting characters or symbols.}
+#'   \item{`pch`}{A vector of plotting characters or symbols. This can either be
+#'                a single character or an integer code for one of a set of
+#'                graphics symbols.}
 #'   \item{`cex`}{A numerical vector giving the amount by which plotting
 #'                characters and symbols should be scaled relative to the
 #'                default.}
+#'   \item{`col`}{The colors for lines and points. Multiple colors can be
+#'                specified so that each point can be given its own color.}
+#'   \item{`bg`}{The background color for the open plot symbols given by
+#'               `pch = 21:25`.}
 #'  }
 #' @return
 #'  `viz_*()` is called for its side-effects: it results in a graphic
 #'  being displayed. Invisibly returns `x`.
+#' @note
+#'  Be careful: graphical parameters are silently recycled.
 #' @example inst/examples/ex-plot.R
 #' @author N. Frerebeau
 #' @docType methods
@@ -612,48 +614,28 @@ setGeneric(
 #' Visualize Variables Factor Map
 #'
 #' Plots column/variable principal coordinates.
-#' @param x A [`CA-class`] or [`PCA-class`] object.
-#' @param axes A length-two [`numeric`] vector giving the dimensions to be
-#'  plotted.
-#' @param active A [`logical`] scalar: should the active observations be
-#'  plotted?
-#' @param sup A [`logical`] scalar: should the supplementary observations be
-#'  plotted?
-#' @param labels A [`logical`] scalar: should labels be drawn?
-#' @param map_color,map_shape,map_size,map_linetype,map_linewidth A vector
-#'  specifying the information to be highlighted. It will be mapped to the
-#'  corresponding aesthetic (see examples and vignettes).
-#'  If a single `character` string is passed, it must be one of "`observation`",
-#'  "`mass`", "`sum`", "`contribution`" or "`cos2`" (see details).
-#'  Any unambiguous substring can be given.
-#'  If `NULL` (the default), no highlighting is applied.
-#' @param main A [`character`] string giving a main title for the plot.
-#' @param sub A [`character`] string giving a subtitle for the plot.
-#' @param ... Further [graphical parameters][graphics::par] (see details).
+#' @inheritParams viz_individuals
 #' @details
-#'  Available statistics:
-#'  \describe{
-#'   \item{`observation`}{Whether an observation is active or supplementary.}
-#'   \item{`mass`}{Weight/mass of each observation.}
-#'   \item{`sum`}{Sum of squared coordinates along `axes`.}
-#'   \item{`contribution`}{Joint contributions to the definition of `axes`.}
-#'   \item{`cos2`}{Joint \eqn{cos^2}{cos2} along `axes`.}
-#'  }
-#'
 #'  Commonly used [graphical parameters][graphics::par] are:
 #'  \describe{
-#'   \item{`col`}{The colors for lines and points. Multiple colors can be
-#'                specified so that each point can be given its own color.}
-#'   \item{`pch`}{A vector of plotting characters or symbols.}
+#'   \item{`pch`}{A vector of plotting characters or symbols. This can either be
+#'                a single character or an integer code for one of a set of
+#'                graphics symbols.}
 #'   \item{`cex`}{A numerical vector giving the amount by which plotting
 #'                characters and symbols should be scaled relative to the
 #'                default.}
 #'   \item{`lty`}{A vector of line types.}
 #'   \item{`lwd`}{A vector of line widths.}
+#'   \item{`col`}{The colors for lines and points. Multiple colors can be
+#'                specified so that each point can be given its own color.}
+#'   \item{`bg`}{The background color for the open plot symbols given by
+#'               `pch = 21:25`.}
 #'  }
 #' @return
 #'  `viz_*()` is called for its side-effects: it results in a graphic
 #'  being displayed. Invisibly returns `x`.
+#' @note
+#'  Be careful: graphical parameters are silently recycled.
 #' @example inst/examples/ex-plot.R
 #' @author N. Frerebeau
 #' @docType methods

R/biplot.R

@@ -170,18 +170,15 @@ viz_biplot <- function(coord_row, coord_col, rows = TRUE, columns = TRUE,
   }
 
   ## Labels
-  usr <- graphics::par("usr")
-  xlim <- usr[c(1, 2)]
-  ylim <- usr[c(3, 4)]
   if (!is.null(labels)) {
     labels <- match.arg(labels, several.ok = TRUE)
     if (any(labels == "rows") | any(labels == "individuals")) {
       viz_labels(x = coord_row$x, y = coord_row$y, labels = coord_row$label,
-                 xlim = xlim, ylim = ylim, col = col.rows, ...)
+                 col = col.rows, ...)
     }
     if (any(labels == "columns") | any(labels == "variables")) {
       viz_labels(x = coord_col$x, y = coord_col$y, labels = coord_col$label,
-                 xlim = xlim, ylim = ylim, col = col.columns, ...)
+                 col = col.columns, ...)
     }
   }
 

R/dimensio-internal.R

@@ -7,7 +7,7 @@
 recycle <- function(x, n, verbose = getOption("dimensio.verbose")) {
   if (length(x) >= n) return(x[seq_len(n)])
 
-  if (verbose) {
+  if (verbose && length(x) > 1) {
     arg <- deparse(substitute(x))
     msg <- sprintf("Note that %s was recycled to length %d.", sQuote(arg), n)
     message(msg)
@@ -16,6 +16,20 @@ recycle <- function(x, n, verbose = getOption("dimensio.verbose")) {
   x
 }
 
+#' Rescale Continuous Vector
+#'
+#' Rescales continuous vector to have specified minimum and maximum.
+#' @param x A continuous `vector` of values to manipulate.
+#' @param to A length-two [`numeric`] vector specifying the output range.
+#' @param from A length-two [`numeric`] vector specifying the input range.
+#' @return A [`numeric`] vector.
+#' @keywords internal
+#' @noRd
+scale_range <- function(x, to = c(0, 1),
+                        from = range(x, na.rm = TRUE, finite = TRUE)) {
+  (x - from[1L]) / diff(from) * diff(to) + to[1L]
+}
+
 #' Weighted Column Means and Standard Deviations
 #'
 #' @param x A [`numeric`] matrix.