Add news

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/plotReducedDim.R

@@ -322,9 +322,12 @@ paired_reddim_plot <- function(df_to_plot, to_plot, dimred, percentVar = NULL,
 }
 
 .handle_truncval <- function(col, truncval) {
-    if (is.character(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", "", truncval)) / 100))
+        return (quantile(col, as.numeric(sub("q", "", as.character(truncval))) / 100))
     }
     if (is.numeric(truncval)) {
         # do nothing?

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.