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comparison cummerbund_wrapper.xml @ 8:b0d11fcbc3ac

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cummerbund add MDS and PCA plots, handle errors from R
author Jim Johnson <jj@umn.edu>
date Thu, 11 Oct 2012 15:14:51 -0500
parents 9d25b0fd882b
children b6427cdbf6d4
comparison
equal deleted inserted replaced
7:c2b922c9d545 8:b0d11fcbc3ac
46 <option value="volcano">Volcano</option> 46 <option value="volcano">Volcano</option>
47 <option value="heatmap">Heatmap</option> 47 <option value="heatmap">Heatmap</option>
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>
52 <option value="pca">Principal Component Analysis (PCA) Plot</option>
51 </param> 53 </param>
52 <when value="density"> 54 <when value="density">
53 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> 55 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/>
54 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> 56 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/>
57 </when>
58 <when value="mds">
59 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
60 </when>
61 <when value="pca">
62 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
55 </when> 63 </when>
56 <when value="dispersion"> 64 <when value="dispersion">
57 </when> 65 </when>
58 <when value="fpkmSCV"> 66 <when value="fpkmSCV">
59 </when> 67 </when>
161 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> 169 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/>
162 </when> 170 </when>
163 </conditional> 171 </conditional>
164 </repeat> 172 </repeat>
165 </inputs> 173 </inputs>
166 174 <stdio>
175 <exit_code range="1:" level="fatal" description="CummerBund Error" />
176 </stdio>
167 <outputs> 177 <outputs>
168 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> 178 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
169 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> 179 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
170 </data> 180 </data>
171 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> 181 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
225 #end if 235 #end if
226 236
227 #for $i, $p in enumerate($plots, start=1): 237 #for $i, $p in enumerate($plots, start=1):
228 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) 238 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
229 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) 239 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
230 240 tryCatch({
231 ## Density plot ## 241 ## Density plot ##
232 #if $p.plot['type'] == "density": 242 #if $p.plot['type'] == "density":
233 csDensity(genes(cuff),replicates=$p.plot.replicates) 243 csDensity(genes(cuff),replicates=$p.plot.replicates)
234 devname = dev.off()
235 244
236 ## Dispersion plot ## 245 ## Dispersion plot ##
237 #elif $p.plot['type'] == "dispersion": 246 #elif $p.plot['type'] == "dispersion":
238 dispersionPlot(genes(cuff)) 247 dispersionPlot(genes(cuff))
239 devname = dev.off()
240 248
241 ## Squared Coefficient of Variation plot ## 249 ## Squared Coefficient of Variation plot ##
242 #elif $p.plot['type'] == "fpkmSCV": 250 #elif $p.plot['type'] == "fpkmSCV":
243 fpkmSCVPlot(genes(cuff)) 251 fpkmSCVPlot(genes(cuff))
244 devname = dev.off()
245 252
246 ## Scatter Matrix ## 253 ## Scatter Matrix ##
247 #elif $p.plot['type'] == "scatterMatrix": 254 #elif $p.plot['type'] == "scatterMatrix":
248 csScatterMatrix(genes(cuff)) 255 csScatterMatrix(genes(cuff))
249 devname = dev.off()
250 256
251 ## Boxplot ## 257 ## Boxplot ##
252 #elif $p.plot['type'] == "boxplot": 258 #elif $p.plot['type'] == "boxplot":
253 csBoxplot(genes(cuff)) 259 csBoxplot(genes(cuff))
254 devname = dev.off()
255 260
256 ## Scatter ## 261 ## Scatter ##
257 #elif $p.plot['type'] == "scatter": 262 #elif $p.plot['type'] == "scatter":
258 #if $p.plot.multiple_genes['multiple_genes_selector']: 263 #if $p.plot.multiple_genes['multiple_genes_selector']:
259 myGeneIds &lt;- c() 264 myGeneIds &lt;- c()
263 myGenes &lt;- getGenes(cuff, myGeneIds) 268 myGenes &lt;- getGenes(cuff, myGeneIds)
264 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) 269 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
265 #else 270 #else
266 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) 271 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth})
267 #end if 272 #end if
268 devname = dev.off()
269 273
270 ## Volcano ## 274 ## Volcano ##
271 #elif $p.plot['type'] == "volcano": 275 #elif $p.plot['type'] == "volcano":
272 #if $p.plot.multiple_genes['multiple_genes_selector']: 276 #if $p.plot.multiple_genes['multiple_genes_selector']:
273 myGeneIds &lt;- c() 277 myGeneIds &lt;- c()
277 myGenes &lt;- getGenes(cuff, myGeneIds) 281 myGenes &lt;- getGenes(cuff, myGeneIds)
278 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") 282 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}")
279 #else 283 #else
280 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") 284 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}")
281 #end if 285 #end if
282 devname = dev.off()
283 286
284 ## Heatmap ## 287 ## Heatmap ##
285 #elif $p.plot['type'] == "heatmap": 288 #elif $p.plot['type'] == "heatmap":
286 myGeneIds &lt;- c() 289 myGeneIds &lt;- c()
287 #for $g in $p.plot.genes: 290 #for $g in $p.plot.genes:
288 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']") 291 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
289 #end for 292 #end for
290 myGenes &lt;- getGenes(cuff, myGeneIds) 293 myGenes &lt;- getGenes(cuff, myGeneIds)
291 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") 294 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}")
292 devname = dev.off()
293 295
294 ## Cluster ## 296 ## Cluster ##
295 #elif $p.plot['type'] == "cluster": 297 #elif $p.plot['type'] == "cluster":
296 myGeneIds &lt;- c() 298 myGeneIds &lt;- c()
297 #for $g in $p.plot.genes: 299 #for $g in $p.plot.genes:
298 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']") 300 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
299 #end for 301 #end for
300 myGenes &lt;- getGenes(cuff, myGeneIds) 302 myGenes &lt;- getGenes(cuff, myGeneIds)
301 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") 303 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}")
302 devname = dev.off()
303 304
304 ## Expression Plot ## 305 ## Expression Plot ##
305 #elif $p.plot['type'] == "expressionplot": 306 #elif $p.plot['type'] == "expressionplot":
306 myGeneId &lt;- "$p.plot.gene_id" 307 myGeneId &lt;- "$p.plot.gene_id"
307 myGenes &lt;- getGenes(cuff, myGeneId) 308 myGenes &lt;- getGenes(cuff, myGeneId)
308 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") 309 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}")
309 devname = dev.off()
310 310
311 ## Expression Bar Plot ## 311 ## Expression Bar Plot ##
312 #elif $p.plot['type'] == "expressionbarplot": 312 #elif $p.plot['type'] == "expressionbarplot":
313 myGeneId &lt;- "$p.plot.gene_id" 313 myGeneId &lt;- "$p.plot.gene_id"
314 myGenes &lt;- getGenes(cuff, myGeneId) 314 myGenes &lt;- getGenes(cuff, myGeneId)
315 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") 315 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}")
316
317 ## MDS plot ##
318 #elif $p.plot['type'] == "mds":
319 MDSplot(genes(cuff),replicates=$p.plot.replicates)
320
321 ## PCA plot ##
322 #elif $p.plot['type'] == "pca":
323 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates)
324 #end if
325
326 },error = function(e) {paste("$p.plot['type'] failed: ", e)})
316 devname = dev.off() 327 devname = dev.off()
317 #end if
318 328
319 #end for 329 #end for
320 </configfile> 330 </configfile>
321 </configfiles> 331 </configfiles>
322 332