# HG changeset patch
# User yhoogstrate
# Date 1408969395 14400
# Node ID c5cc1b24f7d8e4c0abaa97dcff79a3036dadff5f
# Parent  f20dc31afd5ed76a336e9df47fbfc33e68fa89f4
Uploaded

diff -r f20dc31afd5e -r c5cc1b24f7d8 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Mon Aug 25 08:14:33 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Mon Aug 25 08:23:15 2014 -0400
@@ -239,8 +239,6 @@
     dev.off()# Kill it
     
     if(output_format_images == "pdf") {
-      capabilities()
-      ##x11()
       pdf(output_MDSplot)
     } else if(output_format_images == "svg") {
       svg(output_MDSplot)
@@ -260,7 +258,15 @@
   
   if(output_BCVplot != "/dev/null") {
     write("Creating Biological coefficient of variation plot",stdout())
-    pdf(output_BCVplot)
+    
+    if(output_format_images == "pdf") {
+      pdf(output_BCVplot)
+    } else if(output_format_images == "svg") {
+      svg(output_BCVplot)
+    } else {
+      png(output_BCVplot)
+    }
+    
     plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
     dev.off()
   }
@@ -281,14 +287,21 @@
   ## todo EXPORT FPKM
   write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
   
-  
   if(output_MAplot != "/dev/null" || output_PValue_distribution_plot != "/dev/null") {
     etable <- topTags(lrt, n=nrow(dge))\$table
     etable <- etable[order(etable\$FDR), ]
     
     if(output_MAplot != "/dev/null") {
       write("Creating MA plot...",stdout())
-      pdf(output_MAplot)
+      
+      if(output_format_images == "pdf") {
+        pdf(output_MAplot)
+      } else if(output_format_images == "svg") {
+        svg(output_MAplot)
+      } else {
+        png(output_MAplot)
+      }
+      
       with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
       with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
       abline(h=c(-1,1), col="blue")
@@ -297,7 +310,15 @@
   
     if(output_PValue_distribution_plot != "/dev/null") {
       write("Creating P-value distribution plot...",stdout())
-      pdf(output_PValue_distribution_plot)
+      
+      if(output_format_images == "pdf") {
+        pdf(output_PValue_distribution_plot)
+      } else if(output_format_images == "svg") {
+        svg(output_PValue_distribution_plot)
+      } else {
+        png(output_PValue_distribution_plot)
+      }
+      
       expressed_genes <- subset(etable, PValue < 0.99)
       h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
       center <- sum(h\$counts) / length(h\$counts)
@@ -315,7 +336,15 @@
   }
   
   if(output_heatmap_plot != "/dev/null") {
-    pdf(output_heatmap_plot,width=10.5)
+    
+    if(output_format_images == "pdf") {
+      pdf(output_heatmap_plot,width=10.5)
+    } else if(output_format_images == "svg") {
+      svg(output_heatmap_plot,width=10.5)
+    } else {
+      png(output_heatmap_plot,width=10.5)
+    }
+    
     etable2 <- topTags(lrt, n=100)\$table
     order <- rownames(etable2)
     cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
@@ -352,24 +381,54 @@
 			</change_format>
 		</data>
 		
-		<data format="${output_format_images}" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
+		<data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
 			<filter>outputs and ("make_output_BCVplot" in outputs)</filter>
+			
+			<change_format>
+				<when input="output_format_images" value="png" format="png" />
+				<when input="output_format_images" value="pdf" format="pdf" />
+				<when input="output_format_images" value="svg" format="svg" />
+			</change_format>
 		</data>
 		
-		<data format="${output_format_images}" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
+		<data format="png" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
 			<filter>outputs and ("make_output_MAplot" in outputs)</filter>
+			
+			<change_format>
+				<when input="output_format_images" value="png" format="png" />
+				<when input="output_format_images" value="pdf" format="pdf" />
+				<when input="output_format_images" value="svg" format="svg" />
+			</change_format>
 		</data>
 		
-		<data format="${output_format_images}" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
+		<data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
 			<filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
+			
+			<change_format>
+				<when input="output_format_images" value="png" format="png" />
+				<when input="output_format_images" value="pdf" format="pdf" />
+				<when input="output_format_images" value="svg" format="svg" />
+			</change_format>
 		</data>
 		
-		<data format="${output_format_images}" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
+		<data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
 			<filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
+			
+			<change_format>
+				<when input="output_format_images" value="png" format="png" />
+				<when input="output_format_images" value="pdf" format="pdf" />
+				<when input="output_format_images" value="svg" format="svg" />
+			</change_format>
 		</data>
 		
-		<data format="${output_format_images}" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
+		<data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
 			<filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
+			
+			<change_format>
+				<when input="output_format_images" value="png" format="png" />
+				<when input="output_format_images" value="pdf" format="pdf" />
+				<when input="output_format_images" value="svg" format="svg" />
+			</change_format>
 		</data>
 		
 		<data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">