From 6cd0c44805246fbb783fbf29632e3e194f2ded2c Mon Sep 17 00:00:00 2001
From: ningbioinfo <ning.liu@adelaide.edu.au>
Date: Fri, 6 Sep 2024 09:40:37 +0930
Subject: [PATCH] update plotRLExpr function by adding the sce_thres parameter.

---
 R/plotRLE.R       | 15 ++++++++++-----
 man/plotRLExpr.Rd |  5 ++++-
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/R/plotRLE.R b/R/plotRLE.R
index d523ad8..4093d00 100644
--- a/R/plotRLE.R
+++ b/R/plotRLE.R
@@ -3,6 +3,8 @@
 #' @param ordannots variables or computations to sort samples by (tidy style).
 #'
 #' @inheritParams drawPCA
+#' @param sce_thresh Integer value. The threshold of sample size for using 
+#' dot plot instead of box plot.
 #' @return a ggplot2 object, containing the RLE plot.
 #' @export
 #'
@@ -59,7 +61,7 @@ setMethod(
 setMethod(
   "plotRLExpr",
   signature("SummarizedExperiment", "ANY"),
-  function(object, ordannots, assay = 1, ...) {
+  function(object, ordannots, assay = 1, sce_thresh = 1000, ...) {
     isSCE <- is(object, "SingleCellExperiment")
 
     # extract sample data
@@ -70,7 +72,8 @@ setMethod(
     # create data structure
     samporder <- orderSamples(sdata, ordannots)
     rledf <- pdataRLE_intl(object, samporder)
-    p1 <- plotRLExpr_intl(rledf, sdata, isSCE = isSCE, ...)
+    p1 <- plotRLExpr_intl(rledf, sdata, isSCE = isSCE, 
+                          sce_thresh = sce_thresh, ...)
 
     return(p1)
   }
@@ -93,11 +96,12 @@ pdataRLE_intl <- function(emat, sampord) {
   return(rledf)
 }
 
-plotRLExpr_intl <- function(plotdf, sdata, isSCE = FALSE, textScale = 1, ...) {
+plotRLExpr_intl <- function(plotdf, sdata, isSCE = FALSE, textScale = 1, 
+                            sce_thresh = 1000, ...) {
 
   # constant - sample size at which standard plot becomes dense
   dense_thresh <- 50
-  sce_thresh <- 1000
+  sce_thresh <- sce_thresh
 
   # extract aes
   aesmap <- rlang::enquos(...)
@@ -106,7 +110,8 @@ plotRLExpr_intl <- function(plotdf, sdata, isSCE = FALSE, textScale = 1, ...) {
   plotdf <- addSampleAnnot(plotdf, sdata)
 
   # compute plot
-  aesmap <- aesmap[!names(aesmap) %in% c("x", "ymin", "ymax", "upper", "middle", "lower")] # remove fixed mappings if present
+  aesmap <- aesmap[!names(aesmap) %in% c("x", "ymin", "ymax", 
+                                         "upper", "middle", "lower")] # remove fixed mappings if present
 
   # split aes params into those that are not aes i.e. static parametrisation
   if (length(aesmap) > 0) {
diff --git a/man/plotRLExpr.Rd b/man/plotRLExpr.Rd
index 2240ba8..ea52ca8 100644
--- a/man/plotRLExpr.Rd
+++ b/man/plotRLExpr.Rd
@@ -13,7 +13,7 @@ plotRLExpr(object, ordannots = c(), ...)
 
 \S4method{plotRLExpr}{ExpressionSet}(object, ordannots = c(), ...)
 
-\S4method{plotRLExpr}{SummarizedExperiment}(object, ordannots, assay = 1, ...)
+\S4method{plotRLExpr}{SummarizedExperiment}(object, ordannots, assay = 1, sce_thresh = 1000, ...)
 }
 \arguments{
 \item{object}{a DGEList, SummarizedExperiment or ExpressionSet object
@@ -25,6 +25,9 @@ containing gene expression data.}
 
 \item{assay}{a numeric or character, specifying the assay to use (for
 \code{SummarizedExperiment} and its derivative classes).}
+
+\item{sce_thresh}{Integer value. The threshold of sample size for using
+dot plot instead of box plot.}
 }
 \value{
 a ggplot2 object, containing the RLE plot.