Merge branch 'develop' into feature-38/rename-functions-2

r-hyperspec · Dec 14, 2021 · 7561cfa · 7561cfa
2 parents 6b147ea + 20131c8
commit 7561cfa
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -98,6 +98,8 @@ Collate:
     'DEPRECATED-ggplot2.R'
     'DEPRECATED-hy_options.R'
     'DEPRECATED-isample.R'
+    'mark_groups_in_dendrogram.R'
+    'DEPRECATED-mark.dendrogram.R'
     'mark_peak.R'
     'DEPRECATED-markpeak.R'
     'cov_pooled.R'
@@ -180,7 +182,6 @@ Collate:
     'plot_map.R'
     'levelplot.R'
     'map_identify.R'
-    'mark_groups_in_dendrogram.R'
     'mean_sd.R'
     'merge.R'
     'mergeextra.R'

diff --git a/NEWS.md b/NEWS.md
@@ -36,6 +36,7 @@
      `hy.getOptions()`       | `hy_get_options()`               |  #21
      `hy.setOptions()`       | `hy_set_options()`               |  #21
      `makeraster()`          | `raster_make()`                  |  #47
+     `mark.dendrogram()`     | `mark_groups_in_dendrogram()`    |  #43
      `markpeak()`            | `mark_peak()`                    |  #44
      `matlab.dark.palette()` | `palette_matlab_dark()`          |  cbeleites/hyperSpec#299, cbeleites/hyperSpec#299, @sangttruong
      `matlab.palette()`      | `palette_matlab()`               |  cbeleites/hyperSpec#208, cbeleites/hyperSpec#299, @sangttruong

diff --git a/R/DEPRECATED-mark.dendrogram.R b/R/DEPRECATED-mark.dendrogram.R
@@ -0,0 +1,35 @@
+#' @name DEPRECATED-mark.dendrogram
+#' @concept deprecated
+#'
+#' @title (DEPRECATED)
+#'        Identifying spectra and spectral data points
+#'
+#' @description
+#' These \pkg{hyperSpec} functions are **deprecated** and not maintained any
+#' more. You should not use these.
+#' Currently they are present due to back-compatibility reasons and will be
+#' removed in the next release of the package.
+#' Please, use the suggested alternative functions instead:
+#'
+#' - [hyperSpec::mark_groups_in_dendrogram()]
+#'
+#'
+#' @param ... arguments to [hyperSpec::mark_groups_in_dendrogram()].
+#'
+#' @include mark_groups_in_dendrogram.R
+#' @export
+mark.dendrogram <- function(...) {
+  hySpc_deprecated("mark_groups_in_dendrogram")
+  mark_groups_in_dendrogram(...)
+}
+
+
+# Unit tests -----------------------------------------------------------------
+
+hySpc.testthat::test(mark.dendrogram) <- function() {
+  context("Deprecated functions")
+
+  test_that("mark.dendrogram() is deprecated", {
+    expect_error(expect_warning(mark.dendrogram(), "deprecated"))
+  })
+}
diff --git a/R/mark_groups_in_dendrogram.R b/R/mark_groups_in_dendrogram.R
@@ -1,7 +1,10 @@
+#' @title Mark groups in [stats::hclust()] dendrograms
+#'
 #' Groups are marked by colored rectangles as well as by their levels
 #'
 #' The dendrogram should be plotted separately, see the example.
-#' @title Mark groups in [stats::hclust()] dendrograms
+#'
+#'
 #' @param dendrogram the dendrogram
 #' @param groups factor giving the the groups to mark
 #' @param col vector with colors for each group
@@ -13,40 +16,45 @@
 #' @param label side label see example
 #' @param label.right should the side labels be at the right side?
 #' @param ... handed to [graphics::rect()] and [graphics::text()]
+#'
 #' @author Claudia Beleites
 #'
 #' @concept plotting
 #' @concept plotting tools
 #'
 #' @export
-#' @rdname mark.dendrogram
+#' @rdname mark_groups_in_dendrogram
 #' @examples
 #'
 #' dend <- hclust(dist_pearson(laser[[]]))
 #' par(xpd = TRUE, mar = c(5.1, 4, 4, 3)) # allows plotting into the margin
 #' plot(dend, hang = -1, labels = FALSE)
 #'
-#' ## mark clusters
+#' # mark clusters
 #' clusters <- as.factor(cutree(dend, k = 4))
 #' levels(clusters) <- LETTERS[1:4]
-#' mark.dendrogram(dend, clusters, label = "cluster")
+#' mark_groups_in_dendrogram(dend, clusters, label = "cluster")
 #'
-#' ## mark independent factor
-#' mark.dendrogram(dend, as.factor(laser[, , 405.36] > 11000),
+#' # mark independent factor
+#' mark_groups_in_dendrogram(dend, as.factor(laser[, , 405.36] > 11000),
 #'   pos.marker = -0.02, pos.text = -0.03
 #' )
 #'
-#' ## mark continuous variable: convert it to a factor and omit labels
-#' mark.dendrogram(dend, cut(laser[[, , 405.36]], 100), palette_alois(100),
-#'   pos.marker = -.015, text.col = NA,
+#' # mark continuous variable: convert it to a factor and omit labels
+#' mark_groups_in_dendrogram(dend, cut(laser[[, , 405.36]], 100),
+#'   palette_alois(100), pos.marker = -.015, text.col = NA,
 #'   label = expression(I[lambda == 405.36 ~ nm]), label.right = FALSE
 #' )
 #' @importFrom utils head tail
-mark.dendrogram <- function(dendrogram, groups, col = seq_along(unique(groups)),
+mark_groups_in_dendrogram <- function(dendrogram, groups,
+                            col = seq_along(unique(groups)),
                             pos.marker = 0,
                             height = 0.025 * max(dendrogram$height),
                             pos.text = -2.5 * height,
-                            border = NA, text.col = "black", label, label.right = TRUE,
+                            border = NA,
+                            text.col = "black",
+                            label,
+                            label.right = TRUE,
                             ...) {
   if (!is.factor(groups)) {
     groups <- as.factor(groups)