fix: use all Heatmap samples when selection blank

NEWS.md

@@ -7,4 +7,5 @@
 ## heatmapSC
 
 * Add `sample.name.column` to select the metadata column used for sample filtering, defaulting to `orig.ident` (#100).
-* Log requested sample filtering and displayed filtered/total cell counts (#101).
+* Log requested sample filtering and displayed filtered/total cell counts (#101).
+* Use all samples when sample selection is blank (#102).

R/Heatmap.R

@@ -4,7 +4,8 @@
 #'  gene or protein expression levels. Method is based on ComplexHeatmap::pheatmap
 #'
 #' @param object Seurat-class object
-#' @param sample.names Sample names
+#' @param sample.names Select which samples to include. Leave blank to use all
+#'   samples.
 #' @param sample.name.column Metadata column containing sample names. Blank
 #'   values default to "orig.ident".
 #' @param metadata Metadata column to plot
@@ -401,6 +402,11 @@ heatmapSC <- function(object,
     stop("Could not find requested sample name column: ", sample.name.column)
   }
 
+  if (length(samples.to.include) == 0) {
+    message("No samples specified. Using all samples.")
+    samples.to.include <- unique(object@meta.data[[sample.name.column]])
+  }
+
   requested.samples <- if (length(samples.to.include) > 0) {
     paste(shQuote(samples.to.include), collapse = ", ")
   } else {

tests/testthat/test-Heatmap.R

@@ -76,6 +76,19 @@ test_that("Heatmap supports a custom sample name column", {
   expect_identical(colnames(cr.object$object@meta.data), metadata.names)
 })
 
+test_that("Heatmap uses all samples when sample selection is blank", {
+  cr.object <- getParamHM("Chariou")
+  cr.object$sample.names <- c("")
+
+  expect_message(
+    output <- do.call(heatmapSC, cr.object),
+    "No samples specified. Using all samples.",
+    fixed = TRUE
+  )
+
+  expect_setequal(colnames(output$data)[-1], rownames(cr.object$object@meta.data))
+})
+
 test_that("Heatmap preserves punctuation in sample names", {
   cr.object <- getParamHM("Chariou")
   sample.column <- "sample.name_1.2"