Mercurial > repos > jjohnson > cummerbund
comparison 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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| 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 |