@@ -212,65 +212,61 @@ This gene was selected in the interactive session.

 ```{r}

 anno_id <- rownames(values$mydst)

-      anno_gene <- values$myannotation$gene_name

-

-      # if(is.null(input$color_by) & input$genefinder!="")

-      #   return(ggplot() + annotate("text",label="Select a factor to plot your gene",0,0) + theme_bw())

-      # if(is.null(input$color_by) & input$genefinder=="")

-      #   return(ggplot() + annotate("text",label="Select a gene and a factor to plot gene",0,0) + theme_bw())

-      # if(input$genefinder=="")

-      #   return(ggplot() + annotate("text",label="Type in a gene name/id",0,0) + theme_bw())

-      # if(!input$genefinder %in% anno_gene & !input$genefinder %in% anno_id)

-      #   return(ggplot() + annotate("text",label="Gene not found...",0,0) + theme_bw())

+anno_gene <- values$myannotation$gene_name

+

+# if(is.null(input$color_by) & input$genefinder!="")

+#   return(ggplot() + annotate("text",label="Select a factor to plot your gene",0,0) + theme_bw())

+# if(is.null(input$color_by) & input$genefinder=="")

+#   return(ggplot() + annotate("text",label="Select a gene and a factor to plot gene",0,0) + theme_bw())

+# if(input$genefinder=="")

+#   return(ggplot() + annotate("text",label="Type in a gene name/id",0,0) + theme_bw())

+# if(!input$genefinder %in% anno_gene & !input$genefinder %in% anno_id)

+#   return(ggplot() + annotate("text",label="Gene not found...",0,0) + theme_bw())

 if(input$genefinder!="") {

-

+  

   if (input$genefinder %in% anno_id) {

     selectedGene <- rownames(values$mydst)[match(input$genefinder,rownames(values$mydst))]

     selectedGeneSymbol <- values$myannotation$gene_name[match(selectedGene,rownames(values$myannotation))]

-    }

-    if (input$genefinder %in% anno_gene) {

+  }

+  if (input$genefinder %in% anno_gene) {

     selectedGeneSymbol <- values$myannotation$gene_name[which(values$myannotation$gene_name==input$genefinder)]

     if (length(selectedGeneSymbol) > 1) return(ggplot() + annotate("text",label=paste0("Type in a gene name/id of the following:\n",paste(selectedGene,collapse=", ")),0,0) + theme_bw())

     selectedGene <- rownames(values$myannotation)[which(values$myannotation$gene_name==input$genefinder)]

-    }

-    genedata <- plotCounts(values$mydds,gene=selectedGene,intgroup = input$color_by,returnData = TRUE)

-    onlyfactors <- genedata[,match(input$color_by,colnames(genedata))]

-    genedata$plotby <- interaction(onlyfactors)

-    

-    if(input$plot_style=="boxplot"){

-    res <- ggplot(genedata,aes_string(x="plotby",y="count",fill="plotby")) +

-      geom_boxplot(outlier.shape = NA,alpha=0.7) + theme_bw()

-    if(input$ylimZero){

-      res <- res + scale_y_log10(name="Normalized counts - log10 scale",limits=c(0.4,NA))

-    } else {

-      res <- res + scale_y_log10(name="Normalized counts - log10 scale")

-    }

-    

-    res <- res +

-      labs(title=paste0("Normalized counts for ",selectedGeneSymbol," - ",selectedGene)) +

-      scale_x_discrete(name="") +

-      geom_jitter(aes_string(x="plotby",y="count"),position = position_jitter(width = 0.1)) +

-      scale_fill_discrete(name="Experimental\nconditions")

-    # exportPlots$genesBoxplot <- res

-    res

-    

-    } else if(input$plot_style=="violin plot"){

-    res <- ggplot(genedata,aes_string(x="plotby",y="count",fill="plotby")) +

-      geom_violin(aes_string(col="plotby"),alpha = 0.6) + theme_bw()

-    if(input$ylimZero){

-      res <- res + scale_y_log10(name="Normalized counts - log10 scale",limits=c(0.4,NA))

-    } else {

-      res <- res + scale_y_log10(name="Normalized counts - log10 scale")

-    }

-    

-    res <- res +

-      labs(title=paste0("Normalized counts for ",selectedGeneSymbol," - ",selectedGene)) +

-      scale_x_discrete(name="") +

-      geom_jitter(aes_string(x="plotby",y="count"),alpha = 0.8,position = position_jitter(width = 0.1)) +

-      scale_fill_discrete(name="Experimental\nconditions") + scale_color_discrete(guide="none")

-    # exportPlots$genefinder <- res

-    res

   }

+  genedata <- plotCounts(values$mydds,gene=selectedGene,intgroup = input$color_by,returnData = TRUE)

+  onlyfactors <- genedata[,match(input$color_by,colnames(genedata))]

+  genedata$plotby <- interaction(onlyfactors)

+  

+  if (input$plot_style == "boxplot") {

+    plot_style <- "boxplot"

+  } else if (input$plot_style == "violin plot") {

+    plot_style <- "violin"

+  } else {

+    plot_style <- "auto"

+  }

+  

+  res <- mosdef::gene_plot(de_container = values$mydds,

+                           gene = selectedGene,

+                           intgroup = input$color_by,

+                           annotation_obj = values$myannotation,

+                           normalized = TRUE,

+                           labels_display = input$addsamplelabels,

+                           plot_type = plot_style)

+  

+  if (input$ylimZero) {

+    res <- res + scale_y_log10(name = "Normalized counts - log10 scale", limits = c(0.4, NA))

+  } else {

+    res <- res + scale_y_log10(name = "Normalized counts - log10 scale")

+  }

+  

+  res <- res +

+    labs(title = paste0("Normalized counts for ", selectedGeneSymbol, " - ", selectedGene)) +

+    scale_x_discrete(name = "") +

+    scale_fill_discrete(name = "Experimental\nconditions")

+  

+  exportPlots$genefinder_countsplot <- res

+  

+  res

 }

 ```