# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1350053762 18000
# Node ID b6427cdbf6d4551b654acb1cc3b265ec5cf9555a
# Parent  b0d11fcbc3acc5f97924ac5fdde4f2cc02fc4ec6
Add MAplot and csDendro

diff -r b0d11fcbc3ac -r b6427cdbf6d4 cummerbund_wrapper.xml
--- a/cummerbund_wrapper.xml	Thu Oct 11 15:14:51 2012 -0500
+++ b/cummerbund_wrapper.xml	Fri Oct 12 09:56:02 2012 -0500
@@ -50,6 +50,8 @@
 					<option value="expressionbarplot">Expression Bar Plot</option>
 					<option value="mds">MultiDimentional Scaling (MDS) Plot</option>
 					<option value="pca">Principal Component Analysis (PCA) Plot</option>
+					<option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
+					<option value="dendrogram">Dendrogram</option>
 				</param>
 				<when value="density">
 					<param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
@@ -61,6 +63,14 @@
 				<when value="pca">
 					<param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
 				</when>
+				<when value="maplot">
+					<param name="x" type="text" label="Sample name 1"/>
+					<param name="y" type="text" label="Sample name 2"/>
+					<param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
+				</when>
+				<when value="dendrogram">
+					<param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
+				</when>
 				<when value="dispersion">
 				</when>
 				<when value="fpkmSCV">
@@ -321,6 +331,14 @@
     ## PCA plot ##
 	#elif $p.plot['type'] == "pca":
 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates)
+
+    ## MAplot plot ##
+	#elif $p.plot['type'] == "maplot":
+MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count})
+
+    ## Dendogram plot ##
+	#elif $p.plot['type'] == "dendrogram":
+csDendro(genes(cuff),replicates=$p.plot.replicates)
 	#end if
 
 },error = function(e) {paste("$p.plot['type'] failed: ", e)})