Add min and max value (#197) (#215)

DESCRIPTION

@@ -12,8 +12,8 @@ Authors@R: c(
         person("Leo", "Lahti", role=c("ctb"), email="[email protected]", comment = c(ORCID = "0000-0001-5537-637X")),
         person("Tuomas", "Borman", role = c("ctb"), comment = c(ORCID = "0000-0002-8563-8884"))
     )
-Version: 1.35.1
-Date: 2025-01-31
+Version: 1.35.2
+Date: 2025-02-11
 License: GPL-3
 Title: Single-Cell Analysis Toolkit for Gene Expression Data in R
 Description: A collection of tools for doing various analyses of

R/plotHighestExprs.R

@@ -110,7 +110,8 @@ plotHighestExprs <- function(object, n = 50, colour_cells_by = color_cells_by,
     ## Create the plot and annotations. 
     plot_most_expressed <- ggplot(df_exprs_by_cell_long, aes_to_use) + geom_point(alpha = 0.6, shape = 124)
     plot_most_expressed <- plot_most_expressed + labs(x=assay.type, y="Feature") + theme_bw(8) +
-        theme(legend.position = c(1, 0), legend.justification = c(1, 0),
+        theme(legend.position.inside = c(1, 0),
+              legend.justification = c(1, 0),
               axis.text.x = element_text(colour = "gray35"),
               axis.text.y = element_text(colour = "gray35"),
               axis.title.x = element_text(colour = "gray35"),

R/plotReducedDim.R

@@ -56,6 +56,7 @@
 #' \code{options(ggrastr.default.dpi)},
 #' for example \code{options(ggrastr.default.dpi=300)}.
 #' @param by_exprs_values Alias for \code{by.assay.type}.
+#' @param min.value,max.value Minimum and maximum values, beyond which \code{colour_by} values (if numeric) are truncated. Can be set to a numeric value to prevent outlying values from skewing the colour scale, or set to quantiles of the \code{colour_by} variable by setting to (e.g.) \code{"q10"} for the 10th quantile.
 #' @param ... Additional arguments for visualization, see
 #' \code{?"\link{scater-plot-args}"} for details.
 #'
@@ -124,7 +125,9 @@ plotReducedDim <- function(
         swap_rownames = NULL, point.padding = NA, force = 1,
         rasterise = FALSE, scattermore = FALSE,
         bins = NULL, summary_fun = "sum", hex = FALSE,
-        by.assay.type=by_exprs_values, ...
+        by.assay.type=by_exprs_values, 
+        min.value=NULL, max.value=NULL,
+        ...
     ) {
 
     ## Extract reduced dimension representation of cells
@@ -162,6 +165,11 @@ plotReducedDim <- function(
     colour_by <- vis_out$colour_by
     shape_by <- vis_out$shape_by
     size_by <- vis_out$size_by
+
+    if (is.numeric(df_to_plot$colour_by)) {
+        df_to_plot$colour_by <- .truncate_values(df_to_plot$colour_by, min.value, max.value)
+
+    }
 
     ## Dispatching to the central plotter in the simple case of two dimensions.
     if (length(to_plot) == 2L) {
@@ -298,3 +306,31 @@ paired_reddim_plot <- function(df_to_plot, to_plot, dimred, percentVar = NULL,
     }
     plot_out
 }
+
+
+
+.truncate_values <- function(values, min.value=NULL, max.value=NULL) {
+    if (!is.null(min.value)) {
+        min.value <- .handle_truncval(unlist(values), min.value)
+        values[values < min.value] <- min.value
+    }
+    if (!is.null(max.value)) {
+        max.value <- .handle_truncval(unlist(values), max.value)
+        values[values > max.value] <- max.value
+    }
+    values
+}
+
+.handle_truncval <- function(col, truncval) {
+    if (is.character(truncval) || is.factor(truncval)) {
+        if (!is.na(as.character(as.numeric(truncval)))) {
+            return (as.character(as.numeric(truncval)))
+        }
+        stopifnot(grepl("q\\d+", truncval))
+        return (quantile(col, as.numeric(sub("q", "", as.character(truncval))) / 100))
+    }
+    if (is.numeric(truncval)) {
+        # do nothing?
+    }
+    truncval
+}

inst/NEWS.Rd

@@ -1,7 +1,14 @@
 \name{NEWS}
 \title{News for Package \pkg{scater}}
 
-\section{Changes in version 1.28.0, Bioconductor 3.17 Release}{
+\section{Changes in version 1.36.0, Bioconductor 3.21 Release}{
+  \itemize{
+    \item Add \code{min.value,max.value} arguments to \code{plotReducedDim}
+    to enable truncating colour scales using a numeric value or a quantile (eg \code{"q10"}).
+  }
+}
+
+\section{Changes in version 1.28.0, Bioconductor 3.18 Release}{
   \itemize{
     \item Change \code{exprs_values} (and similar) to \code{assay.type}.
     \item Tweak colouring of violin plots.

tests/testthat/test-plot-dimred.R

@@ -48,6 +48,19 @@ test_that("we can produce PCA scatterplots", {
     expect_ggplot(plotPCA(example_sce, bins = 10, colour_by = "Gene_0001"))
     expect_ggplot(plotPCA(example_sce, bins = 10, colour_by = "Gene_0001",
                           hex = TRUE))
+
+    # truncating color scale
+    expect_ggplot(plotPCA(example_sce, min.value = 1))
+    expect_ggplot(plotPCA(example_sce, min.value = "1"))
+    expect_ggplot(plotPCA(example_sce, min.value = factor(1)))
+    expect_ggplot(plotPCA(example_sce, min.value = factor("q1")))
+    expect_ggplot(plotPCA(example_sce, min.value = "q1"))
+
+    expect_ggplot(plotPCA(example_sce, max.value = 2))
+    expect_ggplot(plotPCA(example_sce, max.value = "2"))
+    expect_ggplot(plotPCA(example_sce, max.value = factor(2)))
+    expect_ggplot(plotPCA(example_sce, max.value = factor("q90")))
+    expect_ggplot(plotPCA(example_sce, max.value = "q90"))
 })
 
 test_that("we can produce PCA pairplots", {