unit test & docs fixes

HelenaLC · Mar 27, 2024 · 462b121 · 462b121
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -44,7 +44,7 @@ Suggests:
 URL: https://github.com/HelenaLC/CATALYST
 BugReports: https://github.com/HelenaLC/CATALYST/issues
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 License: GPL (>=2)
 Encoding: UTF-8
 LazyData: true
diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+changes in version 1.27.2
+
++ fixed typos in man pages and vignette
++ fixed unit test failures due to 'ggplot2'-updates etc.
++ omit usage of ':::' operator throughout the package
+
 changes in version 1.27.1
 
 + bug fix in 'plotDiffHeatmap': add 'drop=FALSE'

diff --git a/R/assignPrelim.R b/R/assignPrelim.R
@@ -12,23 +12,24 @@
 #' 
 #' @return a \code{SingleCellExperiment} structured as follows: 
 #' \describe{
-#' \item{assays}{
+#' \item{\code{assays}}{
 #' \itemize{
-#' \item{\code{counts} - raw counts}
-#' \item{\code{exprs} - arcsinh-transformed counts}
-#' \item{\code{scaled} - population-wise scaled 
-#' expression using (95\%)-quantiles as boundaries}
+#' \item \code{counts} - raw counts
+#' \item \code{exprs} - arcsinh-transformed counts
+#' \item \code{scaled} - population-wise scaled 
+#' expression using (95\%)-quantiles as boundaries
 #' }
 #' }
 #' \item{\code{colData}}{
 #' \itemize{
-#' \item{bc_id}{numeric verctor of barcode assignments}
-#' \item{delta}{separation between positive and negative barcode populations}
+#' \item \code{bc_id} - numeric vector of barcode assignments
+#' \item \code{delta} - separation between
+#' positive and negative barcode populations
 #' }
 #' }
 #' \item{\code{metadata}}{
 #' \itemize{
-#' \item{bc_key}{the input debarcoding scheme}
+#' \item \code{bc_key} - the input debarcoding scheme
 #' }
 #' }
 #' }

diff --git a/R/clrDR.R b/R/clrDR.R
@@ -33,7 +33,7 @@
 #'   of cells in a given sample/cluster (for \code{by = "sample/cluster_id"}).
 #' @param point_pal,arrow_pal character string of colors to use
 #'   for points and PC loading arrows. Arguments default to
-#'   \code{CATALYST:::.cluster_cols} for clusters,
+#'   \code{.cluster_cols} for clusters (defined internally),
 #'   and \code{brewer.pal}'s \code{"Set3"} for samples.
 #' @inheritParams runDR
 #' @inheritParams pbMDS
@@ -43,7 +43,7 @@
 #' \describe{
 #' \item{The centered log-ratio (CLR)}{
 #' Let \code{k} be one of \eqn{S} samples, \code{k} one of \eqn{K} clusters,
-#' and \code{p(s,k)} be the proprtion of cells from \code{s} in \eqn{k}.
+#' and \code{p(s,k)} be the proportion of cells from \code{s} in \eqn{k}.
 #' The centered log-ratio (CLR) is defined as
 #' \deqn{clr(sk) = log p(s,k) - \sum p(s,k) / K}
 #' and analogous for clusters replacing \code{s} by \code{k} and \code{K} by
@@ -178,7 +178,7 @@ clrDR <- function(x,
     } else lines <- asp <- NULL
 
     # make base plot
-    p <- ggplot(df, aes_string("x", "y", fill = point_col)) +
+    p <- ggplot(df, aes(.data$x, .data$y, fill = .data$point_col)) +
         lines + guides(
             fill = guide_legend(order = 1, ncol = ncol,
                 override.aes = list(alpha = 1, size = 4)),

diff --git a/R/plotAbundances.R b/R/plotAbundances.R
@@ -76,7 +76,7 @@ plotAbundances <- function(x, k = "meta20",
     linkage = c(
         "average", "ward.D", "single", "complete", 
         "mcquitty", "median", "centroid", "ward.D2"),
-    k_pal = CATALYST:::.cluster_cols) {
+    k_pal = .cluster_cols) {
 
     # check validity of input arguments
     by <- match.arg(by)

diff --git a/R/plotCodes.R b/R/plotCodes.R
@@ -42,8 +42,7 @@
 #' @importFrom S4Vectors metadata
 #' @export
 
-plotCodes <- function(x, k = "meta20", 
-    k_pal = CATALYST:::.cluster_cols) {
+plotCodes <- function(x, k = "meta20", k_pal = .cluster_cols) {
 
     # check validity of input arguments
     .check_sce(x, TRUE)
@@ -92,7 +91,7 @@ plotCodes <- function(x, k = "meta20",
     )
 
     # arrange plots side-by-side
-    lgd <- get_legend(ps[[2]])
+    suppressWarnings(lgd <- get_legend(ps[[2]]))
     ps <- lapply(ps, "+", theme(legend.position = "none"))
     plot_grid(
         lgd, ncol = 1, rel_heights = c(1, 5),

diff --git a/R/plotDR.R b/R/plotDR.R
@@ -82,7 +82,7 @@
 plotDR <- function(x, dr = NULL, 
     color_by = "condition", facet_by = NULL, ncol = NULL,
     assay = "exprs", scale = TRUE, q = 0.01, dims = c(1, 2),
-    k_pal = CATALYST:::.cluster_cols, 
+    k_pal = .cluster_cols, 
     a_pal = hcl.colors(10, "Viridis")) {
 
     # check validity of input arguments

diff --git a/R/plotExprHeatmap.R b/R/plotExprHeatmap.R
@@ -141,7 +141,7 @@ plotExprHeatmap <- function(x, features = NULL,
     row_dend = TRUE, col_dend = TRUE, 
     bars = FALSE, perc = FALSE, bin_anno = FALSE,
     hm_pal = rev(brewer.pal(11, "RdYlBu")), 
-    k_pal = CATALYST:::.cluster_cols, m_pal = k_pal,
+    k_pal = .cluster_cols, m_pal = k_pal,
     distance = c(
         "euclidean", "maximum", "manhattan", 
         "canberra", "binary", "minkowski"), 

diff --git a/R/plotFreqHeatmap.R b/R/plotFreqHeatmap.R
@@ -75,7 +75,7 @@ plotFreqHeatmap <- function(x,
     row_dend = TRUE, col_dend = TRUE,
     bars = TRUE, perc = FALSE,
     hm_pal = rev(brewer.pal(11, "RdBu")),
-    k_pal = CATALYST:::.cluster_cols, m_pal = k_pal) {
+    k_pal = .cluster_cols, m_pal = k_pal) {
 
     # check validity of input arguments
     args <- as.list(environment())

diff --git a/R/plotMahal.R b/R/plotMahal.R
@@ -116,7 +116,7 @@ plotMahal <- function(x, which, assay = "exprs", n = 1e3) {
                         legend.key.width = unit(4, "line"),
                         legend.text = element_text(size = 8), 
                         legend.key = element_blank())
-                lgd <- get_legend(foo)
+                suppressWarnings(lgd <- get_legend(foo))
                 first <- FALSE
             }
         }

diff --git a/R/plotMultiHeatmap.R b/R/plotMultiHeatmap.R
@@ -134,7 +134,7 @@ plotMultiHeatmap <- function(x,
     hm1_pal = rev(brewer.pal(11, "RdYlBu")), 
     hm2_pal = if (isTRUE(hm2 == "abundances")) 
         rev(brewer.pal(11, "PuOr")) else hm1_pal,
-    k_pal = CATALYST:::.cluster_cols, m_pal = k_pal,
+    k_pal = .cluster_cols, m_pal = k_pal,
     distance = c(
         "euclidean", "maximum", "manhattan", 
         "canberra", "binary", "minkowski"), 

diff --git a/R/plotScatter.R b/R/plotScatter.R
@@ -67,7 +67,7 @@
 plotScatter <- function(x, chs, color_by = NULL, facet_by = NULL,
     bins = 100, assay = "exprs", 
     label = c("target", "channel", "both"),
-    zeros = FALSE, k_pal = CATALYST:::.cluster_cols) {
+    zeros = FALSE, k_pal = .cluster_cols) {
     # check validity of input arguments
     label <- match.arg(label)
     args <- as.list(environment())

diff --git a/man/assignPrelim.Rd b/man/assignPrelim.Rd
diff --git a/man/clrDR.Rd b/man/clrDR.Rd
diff --git a/man/plotAbundances.Rd b/man/plotAbundances.Rd
diff --git a/man/plotCodes.Rd b/man/plotCodes.Rd
diff --git a/man/plotDR.Rd b/man/plotDR.Rd
diff --git a/man/plotExprHeatmap.Rd b/man/plotExprHeatmap.Rd
diff --git a/man/plotFreqHeatmap.Rd b/man/plotFreqHeatmap.Rd
diff --git a/man/plotMultiHeatmap.Rd b/man/plotMultiHeatmap.Rd
diff --git a/man/plotScatter.Rd b/man/plotScatter.Rd
diff --git a/tests/testthat/test_plotScatter.R b/tests/testthat/test_plotScatter.R
@@ -36,5 +36,5 @@ test_that("plotScatter() - color_by", {
     expect_is(p$scales$scales[[1]], "ScaleContinuous")    
     p <- plotScatter(x, chs, color_by = "bc_id")
     expect_is(p, "ggplot")
-    expect_is(p$guides$colour, "guide")
+    expect_is(p$guides$guides[[1]], "GuideLegend")
 })