From a5d73f6792c3462fb859df7c944362e29ced6a1f Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Sun, 17 Nov 2024 16:17:59 -0800
Subject: [PATCH] Pass additional arguments to pheatmap via plotMarkerHeatmap.

---
 R/plotMarkerHeatmap.R    | 7 +++++--
 man/plotMarkerHeatmap.Rd | 5 ++++-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/R/plotMarkerHeatmap.R b/R/plotMarkerHeatmap.R
index 9b1dfe9..4258e8c 100644
--- a/R/plotMarkerHeatmap.R
+++ b/R/plotMarkerHeatmap.R
@@ -21,6 +21,7 @@
 #' @param top Integer scalar indicating the top most interesting markers to show in the heatmap.
 #' @param num.threads Integer scalar specifying the number to threads to use.
 #' @param BPPARAM Deprecated, use \code{num.threads} instead.
+#' @param ... Additional parameters for heatmap control passed to \code{\link[pheatmap]{pheatmap}}.
 #'
 #' @return 
 #' The output of \code{\link[pheatmap]{pheatmap}} is returned showing the heatmap on the current graphics device.
@@ -59,7 +60,8 @@ plotMarkerHeatmap <- function(
     order.by.summary="min.rank",
     top=20,
     num.threads=bpnworkers(BPPARAM),
-    BPPARAM = SerialParam()) 
+    BPPARAM = SerialParam(),
+    ...) 
 {
     test <- .to_clean_matrix(test, assay.type, check.missing=FALSE)
     all.markers <- metadata(results)$de.genes[[label]]
@@ -125,6 +127,7 @@ plotMarkerHeatmap <- function(
         color=viridis::viridis(25),
         annotation_col=data.frame(labels=predictions, row.names=colnames(test)),
         cluster_col=FALSE,
-        show_colnames=FALSE
+        show_colnames=FALSE,
+        ...
     )
 }
diff --git a/man/plotMarkerHeatmap.Rd b/man/plotMarkerHeatmap.Rd
index 050bb66..8c1954b 100644
--- a/man/plotMarkerHeatmap.Rd
+++ b/man/plotMarkerHeatmap.Rd
@@ -16,7 +16,8 @@ plotMarkerHeatmap(
   order.by.summary = "min.rank",
   top = 20,
   num.threads = bpnworkers(BPPARAM),
-  BPPARAM = SerialParam()
+  BPPARAM = SerialParam(),
+  ...
 )
 }
 \arguments{
@@ -50,6 +51,8 @@ If \code{NULL}, the existing row names of \code{test} are used.}
 \item{num.threads}{Integer scalar specifying the number to threads to use.}
 
 \item{BPPARAM}{Deprecated, use \code{num.threads} instead.}
+
+\item{...}{Additional parameters for heatmap control passed to \code{\link[pheatmap]{pheatmap}}.}
 }
 \value{
 The output of \code{\link[pheatmap]{pheatmap}} is returned showing the heatmap on the current graphics device.