Violin plot is correctly set up

functions.R

@@ -53,38 +53,46 @@ violinPlot <- function(x,
   #' Violin plot with a group variable
   #'
   #' @description Create a violin plot with a possible group variable
+  #' @param x is a factor variable 
+  #' @param y is value
 
   require(ggplot2)
   require(scales)
+
   ifelse(is.null(group), dt <- data.frame(x,y), dt <- data.frame(x,y,group))
   dt$x[is.na(dt$x)] <- "Na"
   dodge <- position_dodge(width=dodge)
+  min_value <- min(y) - (max(y)  - min(y))
+  max_value <- max(y) + (max(y)  - min(y))
+  plot_list <- list()
 
   if(is.null(group)){
-    plot(ggplot(dt, aes(x=as.factor(x), y=y)) +
-         geom_violin(trim=FALSE) +
-         stat_summary(fun.data="mean_sdl", fun.args = list(mult = 1), geom="crossbar", width=width, fill="white") +
-         labs(title=title, x=title.x, y=title.y) +
-         theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
-               panel.background = element_blank(), axis.line = element_line(colour = "black"),
-               strip.background =element_rect(fill="white")))
-  }else{
-    min_value <- min(y)
-    max_value <- max(y)
-    p <- ggplot(dt, aes(x=as.factor(x), y=y)) +labs(title=title, x=title.x, y=title.y, fill=title.group) +
+    p <- ggplot(dt, aes(x=as.factor(x), y=y)) +
+      labs(title=title, x=title.x, y=title.y) +
       theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1), panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
             panel.background = element_blank(), axis.line = element_line(colour = "black"),
             strip.background =element_rect(fill="white")) + ylim(min_value, max_value)
 
-    plot(p +  geom_violin(aes(fill=as.factor(group)), trim=FALSE, position=dodge) +
-         geom_boxplot(aes(group=interaction(group,x), fill=as.factor(group)), width=width, outlier.colour=NA, position=dodge))
-    plot(p + geom_boxplot(aes(fill=as.factor(group)), trim=FALSE, position=dodge) +
-         facet_wrap( ~ as.factor(x), scales="free") +
-         scale_y_continuous(trans=logY))
-    plot(p + geom_violin(aes(fill=as.factor(group)), trim=FALSE, position=dodge) +
-         facet_wrap( ~ as.factor(x), scales="free") +
-         scale_y_continuous(trans=logY))
+    plot_list[["violin_boxplot"]] <- p + geom_violin(trim=FALSE) + geom_boxplot(width=width, outlier.colour=NA, position=dodge) + facet_wrap( ~ as.factor(x), scales="free")
+    plot_list[["boxplot"]] <- p + geom_boxplot(width=width, outlier.colour=NA, position=dodge) + facet_wrap( ~ as.factor(x), scales="free") + ylim(min(y), max(y))
+    plot_list[["violin"]] <- p + geom_violin(trim=FALSE) + facet_wrap( ~ as.factor(x), scales="free") + facet_wrap( ~ as.factor(x), scales="free")
+  }else{
+    p <- ggplot(dt, aes(x=as.factor(x), y=y)) +labs(title=title, x=title.x, y=title.y, fill=title.group) +
+      theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1), panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
+            panel.background = element_blank(), axis.line = element_line(colour = "black"),
+            strip.background = element_rect(fill="white")) +
+            ylim(min_value, max_value)
+
+    plot_list[["violin_boxplot"]] <- p +  geom_violin(aes(fill=as.factor(group)), trim=FALSE, position=dodge) +
+      geom_boxplot(aes(group=interaction(group,x), fill=as.factor(group)), width=width, outlier.colour=NA, position=dodge)
+    plot_list[["boxplot"]] <- p + geom_boxplot(aes(fill=as.factor(group)), width=width, trim=FALSE, position=dodge) +
+      facet_wrap( ~ as.factor(x), scales="free") +
+      scale_y_continuous(trans=logY) + ylim(min(y), max(y))
+    plot_list[["violin"]] <- p + geom_violin(aes(fill=as.factor(group)), trim=FALSE, position=dodge) +
+      facet_wrap( ~ as.factor(x), scales="free") +
+      scale_y_continuous(trans=logY)
   } 
+  return(plot_list)
 }
 
 splitDf <- function(df, annot, n_samples, n_genes, common_row = NULL){