Mercurial > repos > yhoogstrate > edger_with_design_matrix

changeset 93:31335aa52b2e draft

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Uploaded
author yhoogstrate
date Wed, 18 Mar 2015 06:40:01 -0400
parents 86c3aaa205b5
children 46745f5666ac
files edgeR_Convert_DGE_Table_to_Bedgraph.xml edgeR_Differential_Gene_Expression.xml
diffstat 2 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Fri Mar 13 05:45:09 2015 -0400
+++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Wed Mar 18 06:40:01 2015 -0400
@@ -46,23 +46,23 @@
 	</inputs>
 	
 	<outputs>
-		<data fromat="bedgraph" name="logfc" label="logFC from ${cpm_table.name}">
+		<data format="bedgraph" name="logfc" label="logFC from ${cpm_table.name}">
 			<filter>"c3" in columns</filter>
 		</data>
 		
-		<data fromat="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}">
+		<data format="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}">
 			<filter>"c4" in columns</filter>
 		</data>
 		
-		<data fromat="bedgraph" name="lr" label="LR from ${cpm_table.name}">
+		<data format="bedgraph" name="lr" label="LR from ${cpm_table.name}">
 			<filter>"c5" in columns</filter>
 		</data>
 		
-		<data fromat="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}">
+		<data format="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}">
 			<filter>"c6" in columns</filter>
 		</data>
 		
-		<data fromat="bedgraph" name="fdr" label="FDR from ${cpm_table.name}">
+		<data format="bedgraph" name="fdr" label="FDR from ${cpm_table.name}">
 			<filter>"c7" in columns</filter>
 		</data>
 	</outputs>
--- a/edgeR_Differential_Gene_Expression.xml	Fri Mar 13 05:45:09 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Mar 18 06:40:01 2015 -0400
@@ -274,10 +274,13 @@
   
   if(output_MDSplot_bcv != "/dev/null") {
     write("Creating MDS plot (bcv method)",stdout())
-    pdf("/home/youri/Desktop/bcvmds.pdf")
-    points &lt;- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
+    
+    ## 1. First create a virtual plot to obtain the desired coordinates
+    pdf("bcvmds.pdf")
+    points &lt;- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))
     dev.off()# Kill it
     
+    ## 2. Re-plot the coordinates in a new figure with the size and settings.
     if(output_format_images == "pdf") {
       pdf(output_MDSplot_bcv,height=14,width=14)
     } else if(output_format_images == "svg") {