update visualize.rank(): add ...

Author: Carol-seven

R/visualizations.R

@@ -429,6 +429,8 @@ visualize.ma <- function(dataSet, M.thres = 1) {
 #' 
 #' @param color A string (default = red") specifying the color used to highlight proteins.
 #' 
+#' @param ... Optional arguments passed to \code{\link[ggrepel]{geom_text_repel}}.
+#' 
 #' @return
 #' An object of class \code{ggplot}.
 #' 
@@ -437,7 +439,8 @@ visualize.ma <- function(dataSet, M.thres = 1) {
 #' @export
 
 visualize.rank <- function(dataSet, listName = NULL, regexName = NULL, by = NULL,
-                           facet = c("Condition", "Replicate"), color = "red") {
+                           facet = c("Condition", "Replicate"), color = "red",
+                           ...) {
 
   information <- read.csv("preprocess_protein_information.csv", check.names = FALSE)
   scaffoldCheck <- any(colnames(information) == "Visible?")
@@ -514,7 +517,8 @@ visualize.rank <- function(dataSet, listName = NULL, regexName = NULL, by = NULL
   }
 
   if (length(unionName) > 1) {
-    plot <- plot + geom_text_repel(data = plotData, aes(label = Label), size = 2.5, show.legend = FALSE)
+    plot <- plot + geom_text_repel(data = plotData, aes(label = Label),
+                                   size = 2.5, show.legend = FALSE, ...)
   }
 
   return(plot)

docs/pkgdown.yml

@@ -14,7 +14,7 @@ articles:
   summarization: summarization.html
   transformation: transformation.html
   visualization: visualization.html
-last_built: 2026-02-11T20:42Z
+last_built: 2026-02-11T21:11Z
 urls:
   reference: https://uconn-scs.github.io/msDiaLogue/reference
   article: https://uconn-scs.github.io/msDiaLogue/articles

docs/reference/visualize.rank.html

@@ -12,7 +12,8 @@ visualize.rank(
   regexName = NULL,
   by = NULL,
   facet = c("Condition", "Replicate"),
-  color = "red"
+  color = "red",
+  ...
 )
 ```
 
@@ -56,6 +57,11 @@ visualize.rank(
   A string (default = red") specifying the color used to highlight
   proteins.
 
+- ...:
+
+  Optional arguments passed to
+  [`geom_text_repel`](https://ggrepel.slowkow.com/reference/geom_text_repel.html).
+
 ## Value
 
 An object of class `ggplot`.