Mercurial > repos > jjohnson > cummerbund
diff cummerbund_wrapper.xml @ 9:b6427cdbf6d4
Add MAplot and csDendro
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 12 Oct 2012 09:56:02 -0500 |
| parents | b0d11fcbc3ac |
| children | 2d7eee38ab5b |
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--- 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)})