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comparison cummerbund_wrapper.xml @ 6:137aab1d9ac1

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Add metadata to datatype: CuffDataDB
author Jim Johnson <jj@umn.edu>
date Mon, 18 Nov 2013 16:43:15 -0600
parents f109453ecfa2
children
comparison
equal deleted inserted replaced
5:2bb88bf1c1dd 6:137aab1d9ac1
299 samples(cuff) 299 samples(cuff)
300 print("REPLICATES:") 300 print("REPLICATES:")
301 replicates(cuff) 301 replicates(cuff)
302 print("FEATURES:") 302 print("FEATURES:")
303 print(annotation(genes(cuff))) 303 print(annotation(genes(cuff)))
304 cat(annotation(genes(cuff))[[1]],sep=",")
304 sink() 305 sink()
305 306
306 #for $i, $p in enumerate($plots, start=1): 307 #for $i, $p in enumerate($plots, start=1):
307 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) 308 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
308 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) 309 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
353 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") 354 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}")
354 #end if 355 #end if
355 356
356 ## Heatmap ## 357 ## Heatmap ##
357 #elif $p.plot['type'] == "heatmap": 358 #elif $p.plot['type'] == "heatmap":
359 #if $p.plot.genes and len($p.plot.genes) > 0:
358 myGeneIds &lt;- c() 360 myGeneIds &lt;- c()
359 #for $g in $p.plot.genes: 361 #for $g in $p.plot.genes:
360 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']") 362 myGeneIds &lt;- c(myGeneIds, "$g['gene_id']")
361 #end for 363 #end for
362 myGenes &lt;- getGenes(cuff, myGeneIds) 364 myGenes &lt;- getGenes(cuff, myGeneIds)
365 #else
366 myGenes &lt;- getGenes(cuff,annotation(genes(cuff))[[1]])
367 #end if
363 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") 368 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}")
364 369
365 ## Cluster ## 370 ## Cluster ##
366 #elif $p.plot['type'] == "cluster": 371 #elif $p.plot['type'] == "cluster":
367 myGeneIds &lt;- c() 372 myGeneIds &lt;- c()