Specify geom in plotGenes

R/plotGenes.R

@@ -1,19 +1,23 @@
 #'
 #' plotGenes
 #' 
-#' plot the violin plot for specific genes
+#' @description Plot the plot for specific genes
+#' @details Plot the gene copy number between groups based on the specified geom.
+#' The default is to use gene copy number, but gene family abundance can also be specified.
 #' 
 #' @param stana stana object
 #' @param species candidate species
 #' @param geneID gene ID to be plotted
 #' @param cl named list of clusters
 #' @param target genes or KOs (gene families)
 #' @param return_df return data only
+#' @param geom default to geom_violin, can be changed to the geom like `geom_boxplot`
 #' @import ggplot2
 #' @export
 #' @return ggplot
 #' 
-plotGenes <- function(stana, species, geneID, target="genes", cl=NULL, return_df=FALSE) {
+plotGenes <- function(stana, species, geneID, target="genes", cl=NULL, return_df=FALSE,
+    geom=geom_violin()) {
 	if (is.null(cl)) { cl <- stana@cl}
 	if (target=="genes") {
     	geneDf <- stana@genes[[species]]
@@ -35,7 +39,7 @@ plotGenes <- function(stana, species, geneID, target="genes", cl=NULL, return_df
 
 	ggplot(df, aes(x=group, y=value,
 		fill=group)) +
-	geom_violin()+
+	geom+
 	geom_jitter(shape=21, size=2)+
 	scale_fill_manual(values=stana@colors)+
 	facet_wrap(.~geneID)+