From 4dacca630ba12a9509f2855d4cfc06eaf816e333 Mon Sep 17 00:00:00 2001
From: nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Date: Tue, 22 Oct 2024 18:45:15 +0200
Subject: [PATCH] Remove 'subset' argument in barplot()

---
 R/AllGenerics.R            |  3 +--
 R/barplot.R                | 31 +++++++++++--------------------
 inst/examples/ex-barplot.R |  3 ++-
 man/barplot.Rd             |  8 +++-----
 4 files changed, 17 insertions(+), 28 deletions(-)

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index 63e7b9a..7e1ab1b 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -1038,7 +1038,6 @@ NULL
 #'
 #' Displays a compositional bar chart.
 #' @param height A [`CompositionMatrix-class`] object.
-#' @param select A vector of column indices.
 #' @param by A `vector` of grouping elements, as long as the variables in
 #'  `height`.
 #' @param order_columns A [`logical`] scalar: should should columns be reorderd?
@@ -1057,7 +1056,7 @@ NULL
 #' @param border The color to draw the borders.
 #' @param axes A [`logical`] scalar: should axes be drawn on the plot?
 #' @param legend A [`logical`] scalar: should the legend be displayed?
-#' @param ... Further parameters to be passed to [graphics::barplot()].
+#' @param ... Further graphical parameters.
 #' @return
 #'  `barplot()` is called for its side-effects: is results in a graphic being
 #'  displayed (invisibly return `height`).
diff --git a/R/barplot.R b/R/barplot.R
index 763dbef..4544e3d 100644
--- a/R/barplot.R
+++ b/R/barplot.R
@@ -5,28 +5,20 @@ NULL
 # CompositionMatrix ============================================================
 #' @export
 #' @method barplot CompositionMatrix
-barplot.CompositionMatrix <- function(height, ..., select = NULL,
+barplot.CompositionMatrix <- function(height, ...,
                                       by = groups(height),
                                       order_columns = FALSE, order_rows = NULL,
                                       decreasing = TRUE,
                                       space = 0.2, offset = 0.025,
                                       color = palette_color_discrete(),
                                       border = NA, axes = TRUE, legend = TRUE) {
-  ## Get data
-  if (is.null(select)) select <- seq_len(ncol(height))
-  z <- height[, select, drop = FALSE]
-  if (ncol(z) == 1) {
-    warning("Only one part is selected. Displaying all data.", call. = FALSE)
-    z <- height
-  }
-  n <- nrow(z)
-
   ## Prepare data
-  xy <- prepare_barplot(z, groups = by, order_columns = order_columns,
+  xy <- prepare_barplot(height, groups = by, order_columns = order_columns,
                         order_rows = order_rows, decreasing = decreasing,
                         offset = offset)
   parts <- factor(xy$data$column, levels = colnames(height))
   col <- color(parts)
+  n <- nrow(height)
 
   ## Graphical parameters
   cex.axis <- list(...)$cex.axis %||% graphics::par("cex.axis")
@@ -37,7 +29,7 @@ barplot.CompositionMatrix <- function(height, ..., select = NULL,
   mfrow <- graphics::par("mfrow")
   mar <- graphics::par("mar")
   mar[1] <- 3
-  mar[2] <- width2line(rownames(z), cex = cex.axis) + 0.1
+  mar[2] <- width2line(rownames(height), cex = cex.axis) + 0.1
   mar[3] <- height2line("M", cex = cex.axis)
   mar[4] <- height2line("M", cex = cex.axis)
 
@@ -107,12 +99,12 @@ prepare_barplot <- function(x, groups = NULL,
                             decreasing = TRUE, offset = 0.025) {
   ## Validation
   stopifnot(methods::is(x, "CompositionMatrix"))
-  m <- nrow(x)
+  n <- nrow(x)
 
   ## Grouping
   grp <- as_groups(groups, drop_na = FALSE)
-  if (nlevels(grp) == 0 || nlevels(grp) == m) grp <- rep("", m)
-  arkhe::assert_length(grp, m)
+  if (nlevels(grp) == 0 || nlevels(grp) == n) grp <- rep("", n)
+  arkhe::assert_length(grp, n)
 
   ## Row order
   spl <- lapply(
@@ -139,9 +131,7 @@ prepare_barplot <- function(x, groups = NULL,
   }
 
   ## Relative frequencies
-  freq <- z / rowSums(z)
-  xmax <- t(apply(X = freq, MARGIN = 1, FUN = cumsum))
-  xmin <- xmax - freq
+  z <- z / rowSums(z)
 
   ## Build a long table
   row <- row(z, as.factor = TRUE)
@@ -149,10 +139,11 @@ prepare_barplot <- function(x, groups = NULL,
   data <- data.frame(
     row = as.vector(row),
     column = as.vector(col),
-    value = as.vector(freq)
+    value = as.vector(z)
   )
 
-  n <- nrow(freq)
+  xmax <- t(apply(X = z, MARGIN = 1, FUN = cumsum))
+  xmin <- xmax - z
   data$xmin <- as.vector(xmin)
   data$xmax <- as.vector(xmax)
   data$y <- as.vector(n + 1 - as.numeric(row)) / n # Reverse levels order
diff --git a/inst/examples/ex-barplot.R b/inst/examples/ex-barplot.R
index 23b4fe4..7b07211 100644
--- a/inst/examples/ex-barplot.R
+++ b/inst/examples/ex-barplot.R
@@ -16,4 +16,5 @@ coda <- as_composition(kommos, groups = 1) # Coerce to compositional data
 barplot(coda, order_columns = TRUE)
 
 ## Display only minor elements
-barplot(coda, select = is_element_minor(coda), order_columns = TRUE)
+minor <- coda[, is_element_minor(coda)]
+barplot(minor, order_columns = TRUE)
diff --git a/man/barplot.Rd b/man/barplot.Rd
index 8af1a72..805fd0d 100644
--- a/man/barplot.Rd
+++ b/man/barplot.Rd
@@ -9,7 +9,6 @@
 \S4method{barplot}{CompositionMatrix}(
   height,
   ...,
-  select = NULL,
   by = groups(height),
   order_columns = FALSE,
   order_rows = NULL,
@@ -25,9 +24,7 @@
 \arguments{
 \item{height}{A \code{\linkS4class{CompositionMatrix}} object.}
 
-\item{...}{Further parameters to be passed to \code{\link[graphics:barplot]{graphics::barplot()}}.}
-
-\item{select}{A vector of column indices.}
+\item{...}{Further graphical parameters.}
 
 \item{by}{A \code{vector} of grouping elements, as long as the variables in
 \code{height}.}
@@ -83,7 +80,8 @@ coda <- as_composition(kommos, groups = 1) # Coerce to compositional data
 barplot(coda, order_columns = TRUE)
 
 ## Display only minor elements
-barplot(coda, select = is_element_minor(coda), order_columns = TRUE)
+minor <- coda[, is_element_minor(coda)]
+barplot(minor, order_columns = TRUE)
 }
 \seealso{
 Other plot methods: