From 3fcf87a17521d1343a6eb04e2ee65609401ed9a7 Mon Sep 17 00:00:00 2001
From: noriakis <31095487+noriakis@users.noreply.github.com>
Date: Sun, 21 Apr 2024 21:02:16 +0900
Subject: [PATCH] Specify geom in plotGenes

---
 R/plotGenes.R    | 10 +++++++---
 man/plotGenes.Rd | 11 +++++++++--
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/R/plotGenes.R b/R/plotGenes.R
index 44e7392..00259d0 100644
--- a/R/plotGenes.R
+++ b/R/plotGenes.R
@@ -1,7 +1,9 @@
 #'
 #' 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
@@ -9,11 +11,13 @@
 #' @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)+
diff --git a/man/plotGenes.Rd b/man/plotGenes.Rd
index 6bd4266..2dc244b 100644
--- a/man/plotGenes.Rd
+++ b/man/plotGenes.Rd
@@ -10,7 +10,8 @@ plotGenes(
   geneID,
   target = "genes",
   cl = NULL,
-  return_df = FALSE
+  return_df = FALSE,
+  geom = geom_violin
 )
 }
 \arguments{
@@ -25,10 +26,16 @@ plotGenes(
 \item{cl}{named list of clusters}
 
 \item{return_df}{return data only}
+
+\item{geom}{default to geom_violin, can be changed to the geom like `geom_boxplot`}
 }
 \value{
 ggplot
 }
 \description{
-plot the violin plot for specific genes
+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.
 }