Fix graphical parameters

R/AllGenerics.R

@@ -559,21 +559,15 @@ NULL
 #'  plotted?
 #' @param labels A [`logical`] scalar: should labels be drawn?
 #' @param map_alpha,map_color,map_shape,map_size A vector specifying the
-#'  information to be highlighted.
-#'  It will be mapped to the corresponding aesthetic, according to the
-#'  corresponding `scale` argument (see examples and vignettes).
+#'  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 scale_color The colors for points. Multiple colors can be
-#'  specified so that each point can be given its own color.
-#' @param scale_shape A vector of plotting characters or symbols.
-#' @param scale_size A `numeric` vector giving the amount by which plotting
-#'  characters and symbols should be scaled relative to the default.
 #' @param main A [`character`] string giving a main title for the plot.
 #' @param sub A [`character`] string giving a subtitle for the plot.
-#' @param ... Currently not used.
+#' @param ... Further [graphical parameters][graphics::par] (see details).
 #' @details
 #'  Available statistics:
 #'  \describe{
@@ -583,6 +577,16 @@ NULL
 #'   \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{`cex`}{A numerical vector giving the amount by which plotting
+#'                characters and symbols should be scaled relative to the
+#'                default.}
+#'  }
 #' @return
 #'  `viz_*()` is called for its side-effects: it results in a graphic
 #'  being displayed. Invisibly returns `x`.
@@ -615,22 +619,15 @@ setGeneric(
 #'  plotted?
 #' @param labels A [`logical`] scalar: should labels be drawn?
 #' @param map_alpha,map_color,map_linetype,map_shape,map_size A vector
-#'  specifying the information to be highlighted.
-#'  It will be mapped to the corresponding aesthetic, according to the
-#'  corresponding `scale` argument (see examples and vignettes).
+#'  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 scale_color The colors for points. Multiple colors can be
-#'  specified so that each point can be given its own color.
-#' @param scale_linetype A vector of line type specification.
-#' @param scale_shape A vector of plotting characters or symbols.
-#' @param scale_size A `numeric` vector giving the amount by which plotting
-#'  characters and symbols should be scaled relative to the default.
 #' @param main A [`character`] string giving a main title for the plot.
 #' @param sub A [`character`] string giving a subtitle for the plot.
-#' @param ... Currently not used.
+#' @param ... Further [graphical parameters][graphics::par] (see details).
 #' @details
 #'  Available statistics:
 #'  \describe{
@@ -640,6 +637,18 @@ setGeneric(
 #'   \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{`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.}
+#'  }
 #' @return
 #'  `viz_*()` is called for its side-effects: it results in a graphic
 #'  being displayed. Invisibly returns `x`.

R/biplot.R

@@ -12,7 +12,7 @@ setMethod(
   definition = function(x, axes = c(1, 2),
                         type = c("rows", "columns", "contributions"),
                         active = TRUE, sup = TRUE,
-                        labels = c("rows", "columns"),
+                        labels = "columns",
                         col.rows = "#004488", col.columns = "#BB5566",
                         pch.rows = 16, pch.columns = 17,
                         main = NULL, sub = NULL, ...) {

R/dimensio-internal.R

@@ -6,6 +6,18 @@
 
 `%notin%` <- Negate(`%in%`)
 
+recycle <- function(x, n, verbose = getOption("dimensio.verbose")) {
+  if (length(x) == n) return(x)
+
+  if (verbose) {
+    arg <- deparse(substitute(x))
+    msg <- sprintf("Note that %s was recycled to length %d.", sQuote(arg), n)
+    message(msg)
+  }
+  x <- rep_len(x, length.out = n)
+  x
+}
+
 #' Weighted Column Means and Standard Deviations
 #'
 #' @param x A [`numeric`] matrix.

R/viz_coordinates.R

@@ -13,16 +13,11 @@ setMethod(
                         labels = FALSE,
                         map_alpha = NULL, map_color = NULL,
                         map_shape = NULL, map_size = NULL,
-                        scale_color = NULL, scale_shape = NULL,
-                        scale_size = NULL,
                         main = NULL, sub = NULL, ...) {
     viz_points(x, margin = 1, axes = axes,
                active = active, sup = sup, labels = labels,
                map_alpha = map_alpha, map_color = map_color,
                map_shape = map_shape, map_size = map_size,
-               scale_color = scale_color,
-               scale_shape = scale_shape,
-               scale_size = scale_size,
                main = main, sub = sub, ...)
     invisible(x)
   }
@@ -34,13 +29,11 @@ setMethod(
 setMethod(
   f = "viz_rows",
   signature = c(x = "BootstrapCA"),
-  definition = function(x, axes = c(1, 2), scale_color = NULL,
-                        scale_shape = NULL, ...) {
+  definition = function(x, axes = c(1, 2), ...) {
     group <- get_groups(x, margin = 1)
     viz_points(x, margin = 1, axes = axes,
                active = TRUE, sup = TRUE, labels = FALSE,
-               map_color = group, scale_color = scale_color,
-               map_shape = group, scale_shape = scale_shape, ...)
+               map_color = group, map_shape = group, ...)
     invisible(x)
   }
 )
@@ -55,13 +48,11 @@ setMethod(
   definition = function(x, axes = c(1, 2), active = TRUE, sup = TRUE,
                         labels = FALSE, map_alpha = NULL, map_color = NULL,
                         map_shape = NULL, map_size = NULL,
-                        scale_color = NULL, scale_shape = NULL,
-                        scale_size = NULL, main = NULL, sub = NULL, ...) {
+                        main = NULL, sub = NULL, ...) {
     viz_rows(x, axes = axes, active = active, sup = sup, labels = labels,
              map_alpha = map_alpha, map_color = map_color,
              map_shape = map_shape, map_size = map_size,
-             scale_color = scale_color, scale_shape = scale_shape,
-             scale_size = scale_size, main = main, sub = sub, ...)
+             main = main, sub = sub, ...)
     invisible(x)
   }
 )
@@ -77,15 +68,11 @@ setMethod(
   definition = function(x, axes = c(1, 2), active = TRUE, sup = TRUE,
                         labels = FALSE, map_alpha = NULL, map_color = NULL,
                         map_shape = NULL, map_size = NULL,
-                        scale_color = NULL, scale_shape = NULL,
-                        scale_size = NULL, main = NULL, sub = NULL, ...) {
+                        main = NULL, sub = NULL, ...) {
     viz_points(x, margin = 2, axes = axes,
                active = active, sup = sup, labels = labels,
                map_alpha = map_alpha, map_color = map_color,
                map_shape = map_shape, map_size = map_size,
-               scale_color = scale_color,
-               scale_shape = scale_shape,
-               scale_size = scale_size,
                main = main, sub = sub, ...)
     invisible(x)
   }
@@ -97,12 +84,10 @@ setMethod(
 setMethod(
   f = "viz_columns",
   signature = c(x = "BootstrapCA"),
-  definition = function(x, axes = c(1, 2), scale_color = NULL,
-                        scale_shape = NULL, ...) {
+  definition = function(x, axes = c(1, 2), ...) {
     group <- get_groups(x, margin = 2)
     viz_points(x, margin = 2, axes = axes, active = TRUE, sup = TRUE,
-               labels = FALSE, map_color = group, scale_color = scale_color,
-               map_shape = group, scale_shape = scale_shape, ...)
+               labels = FALSE, map_color = group, map_shape = group, ...)
     invisible(x)
   }
 )
@@ -117,17 +102,16 @@ setMethod(
   definition = function(x, axes = c(1, 2), active = TRUE, sup = TRUE,
                         labels = TRUE, map_alpha = NULL, map_color = NULL,
                         map_linetype = NULL, map_size = NULL,
-                        scale_color = NULL, scale_linetype = NULL,
-                        scale_size = NULL, main = NULL, sub = NULL, ...) {
+                        main = NULL, sub = NULL, ...) {
     ## Prepare data
     coord <- prepare_coord(x, margin = 2, axes = axes, active = active,
                            sup = sup)
 
     ## Graphical parameters
     param <- prepare_param(coord, map_alpha = map_alpha,
-                           map_color = map_color, scale_color = scale_color,
-                           map_linetype = map_linetype, scale_linetype = scale_linetype,
-                           map_size = map_size, scale_size = scale_size)
+                           map_color = map_color,
+                           map_linetype = map_linetype,
+                           map_size = map_size, ...)
 
     ## Open new window
     grDevices::dev.hold()
@@ -159,9 +143,8 @@ setMethod(
 
     ## Labels
     if (labels && nrow(coord) > 1) {
-      usr <- graphics::par("usr")
       viz_labels(x = coord$x, y = coord$y, labels = coord$label,
-                 xlim = usr[c(1, 2)], ylim = usr[c(3, 4)], col = param$col)
+                 col = param$col)
     }
 
     ## Evaluate post-plot and pre-axis expressions
@@ -197,40 +180,34 @@ setMethod(
 setMethod(
   f = "viz_variables",
   signature = c(x = "BootstrapPCA"),
-  definition = function(x, axes = c(1, 2), scale_color = NULL,
-                        scale_shape = NULL, ...) {
+  definition = function(x, axes = c(1, 2), ...) {
     group <- get_groups(x, margin = 2)
     viz_points(x, margin = 2, axes = axes, active = TRUE, sup = TRUE,
-               labels = FALSE, map_color = group, scale_color = scale_color,
-               map_shape = group, scale_shape = scale_shape, ...)
+               labels = FALSE, map_color = group, map_shape = group, ...)
     invisible(x)
   }
 )
 
 # Helpers ======================================================================
 viz_points <- function(x, margin, axes, active = TRUE, sup = TRUE, labels = FALSE,
-                       map_alpha = NULL, map_color = NULL, scale_color = NULL,
-                       map_shape = NULL, scale_shape = NULL,
-                       map_size = NULL, scale_size = NULL,
-                       main = NULL, sub = NULL, ...) {
+                       map_alpha = NULL, map_color = NULL, map_shape = NULL,
+                       map_size = NULL, main = NULL, sub = NULL, ...) {
   ## Prepare data
   coord <- prepare_coord(x, margin = margin, axes = axes, active = active,
                          sup = sup)
 
   ## Graphical parameters
-  param <- prepare_param(coord, map_alpha = map_alpha,
-                         map_color = map_color, scale_color = scale_color,
-                         map_shape = map_shape, scale_shape = scale_shape,
-                         map_size = map_size, scale_size = scale_size)
+  param <- prepare_param(coord, map_alpha = map_alpha, map_color = map_color,
+                         map_shape = map_shape, map_size = map_size, ...)
 
   ## Open new window
   grDevices::dev.hold()
   on.exit(grDevices::dev.flush(), add = TRUE)
   graphics::plot.new()
 
   ## Set plotting coordinates
-  xlim <- range(coord$x)
-  ylim <- range(coord$y)
+  xlim <- range(coord$x, na.rm = TRUE)
+  ylim <- range(coord$y, na.rm = TRUE)
   graphics::plot.window(xlim = xlim, ylim = ylim, asp = 1)
 
   ## Evaluate pre-plot expressions
@@ -244,9 +221,8 @@ viz_points <- function(x, margin, axes, active = TRUE, sup = TRUE, labels = FALS
 
   ## Labels
   if (labels) {
-    usr <- graphics::par("usr")
     viz_labels(x = coord$x, y = coord$y, labels = coord$label,
-               xlim = usr[c(1, 2)], ylim = usr[c(3, 4)], col = param$col, ...)
+               col = param$col, ...)
   }
 
   ## Evaluate post-plot and pre-axis expressions
@@ -339,19 +315,17 @@ prepare_coord <- function(object, margin, axes = c(1, 2), active = TRUE,
   data
 }
 
-prepare_param <- function(x, map_alpha = NULL,
-                          map_color = NULL, scale_color = NULL,
-                          map_size = NULL, scale_size = NULL,
-                          map_linetype = NULL, scale_linetype = NULL,
-                          map_shape = NULL, scale_shape = NULL) {
+prepare_param <- function(x, map_alpha = NULL, map_color = NULL,
+                          map_size = NULL, map_linetype = NULL,
+                          map_shape = NULL, ...) {
   n <- nrow(x)
 
   ## Graphical parameters
-  col <- scale_color
-  pch <- scale_shape
-  lty <- scale_linetype
-  cex <- scale_size %||% graphics::par("cex")
-  lwd <- scale_size %||% graphics::par("lwd")
+  col <- list(...)$col
+  pch <- list(...)$pch
+  lty <- list(...)$lty
+  cex <- list(...)$cex %||% graphics::par("cex")
+  lwd <- list(...)$lwd %||% graphics::par("lwd")
 
   choices <- c("observation", "mass", "sum", "contribution", "cos2")
 
@@ -371,12 +345,13 @@ prepare_param <- function(x, map_alpha = NULL,
     } else {
       ## Discrete scale
       n_col <- length(unique(map_color))
-      if (is.null(col)) col <- grDevices::hcl.colors(n_col, "viridis")
-      if (length(col) < n_col) assert_length(col, n_col)
+      if (is.null(col))
+        col <- grDevices::hcl.colors(n_col, "viridis")
+      col <- recycle(col, n_col)
       col <- col[as.factor(map_color)]
     }
   } else {
-    col <- rep(col %||% graphics::par("col"), n)
+    col <- rep_len(col %||% graphics::par("col"), n)
   }
 
   if (!is.null(map_alpha)) {
@@ -397,10 +372,11 @@ prepare_param <- function(x, map_alpha = NULL,
     }
 
     n_lty <- length(unique(map_linetype))
-    if (is.null(lty)) lty <- seq_along(unique(map_linetype))
+    if (is.null(lty)) lty <- seq_len(n_lty)
+    lty <- recycle(lty, n_lty)
     lty <- lty[as.factor(map_linetype)]
   } else {
-    lty <- rep(lty %||% graphics::par("lty"), n)
+    lty <- rep_len(lty %||% graphics::par("lty"), n)
   }
 
   if (!is.null(map_shape)) {
@@ -409,10 +385,12 @@ prepare_param <- function(x, map_alpha = NULL,
       map_shape <- x[[map_shape]]
     }
 
-    if (is.null(pch)) pch <- seq_along(unique(map_shape))
+    n_pch <- length(unique(map_shape))
+    if (is.null(pch)) pch <- seq_len(n_pch)
+    pch <- recycle(pch, n_pch)
     pch <- pch[as.factor(map_shape)]
   } else {
-    pch <- rep(pch %||% graphics::par("pch"), n)
+    pch <- rep_len(pch %||% graphics::par("pch"), n)
   }
 
   if (!is.null(map_size)) {
@@ -424,8 +402,8 @@ prepare_param <- function(x, map_alpha = NULL,
     cex <- cex + map_size / max(map_size)
     lwd <- lwd + map_size / max(map_size)
   } else {
-    cex <- rep(cex, n)
-    lwd <- rep(lwd, n)
+    cex <- rep_len(cex, n)
+    lwd <- rep_len(lwd, n)
   }
 
   data.frame(col = col, pch = pch, cex = cex, lty = lty, lwd = lwd)