diff edgeR_Differential_Gene_Expression.xml @ 67:6eb298a5561f draft

Uploaded

--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 09:08:16 2014 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 30 09:08:23 2014 -0400
@@ -4,7 +4,8 @@
 	
 	<requirements>
 		<!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
-		<requirement type="package" version="3.1.0">R</requirement>
+		<!--<requirement type="package" version="3.1.0">R</requirement>-->
+		<requirement type="package" version="3.0.3">R</requirement>
 		<requirement type="package" version="latest">package_biocLite_edgeR_limma</requirement>
 	</requirements>
 	
@@ -84,6 +85,11 @@
 			
 			2> stderr.txt ; 
 			
+			#if $output_format_images == "png":
+				convert $output_format_images "{$output_format_images}.png" ; 
+				mv "{$output_format_images}.png" $output_format_images ; 
+			#end if
+			
 			grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
 			
 			## Locale error messages:
@@ -239,13 +245,13 @@
     points &lt;- plotMDS.DGEList(dge,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
     dev.off()# Kill it
     
-    if(output_format_images == "pdf") {
+    if(output_format_images == "pdf" || output_format_images == "png") {
       pdf(output_MDSplot)
     } else if(output_format_images == "svg") {
       svg(output_MDSplot)
-    } else {
-      png(output_MDSplot)
-    }
+    ##} else {
+    ##  png(output_MDSplot)
+    ##}
     
     diff_x &lt;- abs(max(points\$x)-min(points\$x))
     diff_y &lt;-(max(points\$y)-min(points\$y))
@@ -260,13 +266,13 @@
   if(output_BCVplot != "/dev/null") {
     write("Creating Biological coefficient of variation plot",stdout())
     
-    if(output_format_images == "pdf") {
+    if(output_format_images == "pdf" || output_format_images == "png") {
       pdf(output_BCVplot)
     } else if(output_format_images == "svg") {
       svg(output_BCVplot)
-    } else {
-      png(output_BCVplot)
-    }
+    ##} else {
+    ##  png(output_BCVplot)
+    ##}
     
     plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
     dev.off()
@@ -295,13 +301,13 @@
     if(output_MAplot != "/dev/null") {
       write("Creating MA plot...",stdout())
       
-      if(output_format_images == "pdf") {
+      if(output_format_images == "pdf" || output_format_images == "png") {
         pdf(output_MAplot)
       } else if(output_format_images == "svg") {
         svg(output_MAplot)
-      } else {
-        png(output_MAplot)
-      }
+      ##} else {
+      ##  png(output_MAplot)
+      ##}
       
       with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
       with(subset(etable, FDR &lt; fdr), points(logCPM, logFC, pch=20, col="red"))
@@ -312,13 +318,13 @@
     if(output_PValue_distribution_plot != "/dev/null") {
       write("Creating P-value distribution plot...",stdout())
       
-      if(output_format_images == "pdf") {
+      if(output_format_images == "pdf" || output_format_images == "png") {
         pdf(output_PValue_distribution_plot)
       } else if(output_format_images == "svg") {
         svg(output_PValue_distribution_plot)
-      } else {
-        png(output_PValue_distribution_plot)
-      }
+      ##} else {
+      ##  png(output_PValue_distribution_plot)
+      ##}
       
       expressed_genes &lt;- subset(etable, PValue &lt; 0.99)
       h &lt;- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (&lt; 0.99)")
@@ -338,13 +344,13 @@
   
   if(output_heatmap_plot != "/dev/null") {
     
-    if(output_format_images == "pdf") {
+    if(output_format_images == "pdf" || output_format_images == "png") {
       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)
-    }
+    ##} else {
+    ##  png(output_heatmap_plot,width=10.5)
+    ##}
     
     etable2 &lt;- topTags(lrt, n=100)\$table
     order &lt;- rownames(etable2)