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comparison cummerbund_wrapper.xml @ 9:b6427cdbf6d4

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Add MAplot and csDendro
author Jim Johnson <jj@umn.edu>
date Fri, 12 Oct 2012 09:56:02 -0500
parents b0d11fcbc3ac
children 2d7eee38ab5b
comparison
equal deleted inserted replaced
8:b0d11fcbc3ac 9:b6427cdbf6d4
48 <option value="cluster">Cluster</option> 48 <option value="cluster">Cluster</option>
49 <option value="expressionplot">Expression Plot</option> 49 <option value="expressionplot">Expression Plot</option>
50 <option value="expressionbarplot">Expression Bar Plot</option> 50 <option value="expressionbarplot">Expression Bar Plot</option>
51 <option value="mds">MultiDimentional Scaling (MDS) Plot</option> 51 <option value="mds">MultiDimentional Scaling (MDS) Plot</option>
52 <option value="pca">Principal Component Analysis (PCA) Plot</option> 52 <option value="pca">Principal Component Analysis (PCA) Plot</option>
53 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option>
54 <option value="dendrogram">Dendrogram</option>
53 </param> 55 </param>
54 <when value="density"> 56 <when value="density">
55 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> 57 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
56 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> 58 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
57 </when> 59 </when>
58 <when value="mds"> 60 <when value="mds">
59 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> 61 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
60 </when> 62 </when>
61 <when value="pca"> 63 <when value="pca">
64 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
65 </when>
66 <when value="maplot">
67 <param name="x" type="text" label="Sample name 1"/>
68 <param name="y" type="text" label="Sample name 2"/>
69 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
70 </when>
71 <when value="dendrogram">
62 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> 72 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
63 </when> 73 </when>
64 <when value="dispersion"> 74 <when value="dispersion">
65 </when> 75 </when>
66 <when value="fpkmSCV"> 76 <when value="fpkmSCV">
319 MDSplot(genes(cuff),replicates=$p.plot.replicates) 329 MDSplot(genes(cuff),replicates=$p.plot.replicates)
320 330
321 ## PCA plot ## 331 ## PCA plot ##
322 #elif $p.plot['type'] == "pca": 332 #elif $p.plot['type'] == "pca":
323 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates) 333 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates)
334
335 ## MAplot plot ##
336 #elif $p.plot['type'] == "maplot":
337 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count})
338
339 ## Dendogram plot ##
340 #elif $p.plot['type'] == "dendrogram":
341 csDendro(genes(cuff),replicates=$p.plot.replicates)
324 #end if 342 #end if
325 343
326 },error = function(e) {paste("$p.plot['type'] failed: ", e)}) 344 },error = function(e) {paste("$p.plot['type'] failed: ", e)})
327 devname = dev.off() 345 devname = dev.off()
328 346