Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 91:c81da57fff20 draft

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author yhoogstrate
date Mon, 09 Mar 2015 08:35:13 -0400
parents f87938c392bf
children 31335aa52b2e
comparison
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90:f87938c392bf 91:c81da57fff20
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.c"> 2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.0.3-latest.d">
3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description> 3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
4 4
5 <requirements> 5 <requirements>
6 <!--<requirement type="package" version="3.0.1">package_r3_withx</requirement>-->
7 <!--<requirement type="package" version="3.1.0">R</requirement>-->
8 <requirement type="package" version="3.0.3">R</requirement> 6 <requirement type="package" version="3.0.3">R</requirement>
9 <requirement type="package" version="latest">biocLite_edgeR_limma</requirement> 7 <requirement type="package" version="latest">biocLite_edgeR_limma</requirement>
10 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
11 </requirements> 8 </requirements>
12 9
13 <version_command>R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null</version_command> 10 <version_command>R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null</version_command>
14 11
15 <command> 12 <command>
91 #else: 88 #else:
92 > /dev/null 89 > /dev/null
93 #end if 90 #end if
94 91
95 2> stderr.txt ; 92 2> stderr.txt ;
96
97 #if $output_format_images.value == "png":
98 echo "Converting PDF figures to PNG" ;
99
100 #if $output_MDSplot_logFC:
101 #set $output_MDSplot_logFC_tmp = str($output_MDSplot_logFC)+".png"
102
103 gm convert $output_MDSplot_logFC png:$output_MDSplot_logFC_tmp ;
104 mv $output_MDSplot_logFC_tmp $output_MDSplot_logFC ;
105 #end if
106
107 #if $output_MDSplot_bcv:
108 #set $output_MDSplot_bcv_tmp = str($output_MDSplot_bcv)+".png"
109
110 gm convert $output_MDSplot_bcv png:$output_MDSplot_bcv_tmp ;
111 mv $output_MDSplot_bcv_tmp $output_MDSplot_bcv ;
112 #end if
113
114 #if $output_BCVplot:
115 #set $output_BCVplot_tmp = str($output_BCVplot)+".png"
116
117 gm convert $output_BCVplot png:$output_BCVplot_tmp ;
118 mv $output_BCVplot_tmp $output_BCVplot ;
119 #end if
120
121 #if $output_MAplot:
122 #set $output_MAplot_tmp = str($output_MAplot)+".png"
123
124 gm convert $output_MAplot png:$output_MAplot_tmp ;
125 mv $output_MAplot_tmp $output_MAplot ;
126 #end if
127
128 #if $output_PValue_distribution_plot:
129 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
130
131 gm convert $output_PValue_distribution_plot png:$output_PValue_distribution_plot_tmp ;
132 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ;
133 #end if
134
135 #if $output_hierarchical_clustering_plot:
136 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
137
138 gm convert $output_hierarchical_clustering_plot png:$output_hierarchical_clustering_plot_tmp ;
139 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ;
140 #end if
141
142 #if $output_heatmap_plot:
143 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
144
145 gm convert $output_heatmap_plot png:$output_heatmap_plot_tmp ;
146 mv $output_heatmap_plot_tmp $output_heatmap_plot ;
147 #end if
148 #end if
149 93
150 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 94 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
151 95
152 ## Locale error messages: 96 ## Locale error messages:
153 grep -v 'During startup - Warning messages' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 97 grep -v 'During startup - Warning messages' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
304 if(output_MDSplot_logFC != "/dev/null") { 248 if(output_MDSplot_logFC != "/dev/null") {
305 write("Creating MDS plot (logFC method)",stdout()) 249 write("Creating MDS plot (logFC method)",stdout())
306 points &lt;- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot 250 points &lt;- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
307 dev.off()# Kill it 251 dev.off()# Kill it
308 252
309 if(output_format_images == "pdf" || output_format_images == "png") { 253 if(output_format_images == "pdf") {
310 pdf(output_MDSplot_logFC,height=14,width=14) 254 pdf(output_MDSplot_logFC,height=14,width=14)
311 } else if(output_format_images == "svg") { 255 } else if(output_format_images == "svg") {
312 svg(output_MDSplot_logFC,height=14,width=14) 256 svg(output_MDSplot_logFC,height=14,width=14)
257 } else {
258 ## png(output_MDSplot_logFC)
259 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
260
261 bitmap(output_MDSplot_logFC,type="png16m",height=14,width=14)
313 } 262 }
314 ## else { 263
315 ## png(output_MDSplot_logFC)
316 ##}
317 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings
318 264
319 diff_x &lt;- abs(max(points\$x)-min(points\$x)) 265 diff_x &lt;- abs(max(points\$x)-min(points\$x))
320 diff_y &lt;-(max(points\$y)-min(points\$y)) 266 diff_y &lt;-(max(points\$y)-min(points\$y))
321 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2") 267 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
322 points(points\$x,points\$y,pch=20) 268 points(points\$x,points\$y,pch=20)
330 write("Creating MDS plot (bcv method)",stdout()) 276 write("Creating MDS plot (bcv method)",stdout())
331 pdf("/home/youri/Desktop/bcvmds.pdf") 277 pdf("/home/youri/Desktop/bcvmds.pdf")
332 points &lt;- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot 278 points &lt;- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
333 dev.off()# Kill it 279 dev.off()# Kill it
334 280
335 if(output_format_images == "pdf" || output_format_images == "png") { 281 if(output_format_images == "pdf") {
336 pdf(output_MDSplot_bcv,height=14,width=14) 282 pdf(output_MDSplot_bcv,height=14,width=14)
337 } else if(output_format_images == "svg") { 283 } else if(output_format_images == "svg") {
338 svg(output_MDSplot_bcv,height=14,width=14) 284 svg(output_MDSplot_bcv,height=14,width=14)
285 } else {
286 ## png(output_MDSplot_bcv)
287 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
288
289 bitmap(output_MDSplot_bcv,type="png16m",height=14,width=14)
339 } 290 }
340 ## else {
341 ## png(output_MDSplot_bcv)
342 ##}
343 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings
344 291
345 diff_x &lt;- abs(max(points\$x)-min(points\$x)) 292 diff_x &lt;- abs(max(points\$x)-min(points\$x))
346 diff_y &lt;-(max(points\$y)-min(points\$y)) 293 diff_y &lt;-(max(points\$y)-min(points\$y))
347 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2") 294 plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
348 points(points\$x,points\$y,pch=20) 295 points(points\$x,points\$y,pch=20)
354 301
355 302
356 if(output_BCVplot != "/dev/null") { 303 if(output_BCVplot != "/dev/null") {
357 write("Creating Biological coefficient of variation plot",stdout()) 304 write("Creating Biological coefficient of variation plot",stdout())
358 305
359 if(output_format_images == "pdf" || output_format_images == "png") { 306 if(output_format_images == "pdf") {
360 pdf(output_BCVplot) 307 pdf(output_BCVplot)
361 } else if(output_format_images == "svg") { 308 } else if(output_format_images == "svg") {
362 svg(output_BCVplot) 309 svg(output_BCVplot)
310 } else {
311 ## png(output_BCVplot)
312 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
313
314 bitmap(output_BCVplot,type="png16m")
363 } 315 }
364 ##else {
365 ## png(output_BCVplot)
366 ##}
367 316
368 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance") 317 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
369 dev.off() 318 dev.off()
370 } 319 }
371 320
390 etable &lt;- etable[order(etable\$FDR), ] 339 etable &lt;- etable[order(etable\$FDR), ]
391 340
392 if(output_MAplot != "/dev/null") { 341 if(output_MAplot != "/dev/null") {
393 write("Creating MA plot...",stdout()) 342 write("Creating MA plot...",stdout())
394 343
395 if(output_format_images == "pdf" || output_format_images == "png") { 344 if(output_format_images == "pdf") {
396 pdf(output_MAplot) 345 pdf(output_MAplot)
397 } else if(output_format_images == "svg") { 346 } else if(output_format_images == "svg") {
398 svg(output_MAplot) 347 svg(output_MAplot)
348 } else {
349 ## png(output_MAplot)
350 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
351
352 bitmap(output_MAplot,type="png16m")
399 } 353 }
400 ##else {
401 ## png(output_MAplot)
402 ##}
403 354
404 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) 355 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
405 with(subset(etable, FDR &lt; fdr), points(logCPM, logFC, pch=20, col="red")) 356 with(subset(etable, FDR &lt; fdr), points(logCPM, logFC, pch=20, col="red"))
406 abline(h=c(-1,1), col="blue") 357 abline(h=c(-1,1), col="blue")
407 dev.off() 358 dev.off()
408 } 359 }
409 360
410 if(output_PValue_distribution_plot != "/dev/null") { 361 if(output_PValue_distribution_plot != "/dev/null") {
411 write("Creating P-value distribution plot...",stdout()) 362 write("Creating P-value distribution plot...",stdout())
412 363
413 if(output_format_images == "pdf" || output_format_images == "png") { 364 if(output_format_images == "pdf") {
414 pdf(output_PValue_distribution_plot) 365 pdf(output_PValue_distribution_plot,width=14,height=14)
415 } else if(output_format_images == "svg") { 366 } else if(output_format_images == "svg") {
416 svg(output_PValue_distribution_plot) 367 svg(output_PValue_distribution_plot,width=14,height=14)
368 } else {
369 ## png(output_PValue_distribution_plot)
370 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
371
372 bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14)
417 } 373 }
418 ##else {
419 ## png(output_PValue_distribution_plot)
420 ##}
421 374
422 expressed_genes &lt;- subset(etable, PValue &lt; 0.99) 375 expressed_genes &lt;- subset(etable, PValue &lt; 0.99)
423 h &lt;- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (&lt; 0.99)") 376 h &lt;- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (&lt; 0.99)")
424 center &lt;- sum(h\$counts) / length(h\$counts) 377 center &lt;- sum(h\$counts) / length(h\$counts)
425 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2) 378 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2)
435 } 388 }
436 } 389 }
437 390
438 if(output_heatmap_plot != "/dev/null") { 391 if(output_heatmap_plot != "/dev/null") {
439 392
440 if(output_format_images == "pdf" || output_format_images == "png") { 393 if(output_format_images == "pdf") {
441 pdf(output_heatmap_plot,width=10.5) 394 pdf(output_heatmap_plot,width=10.5)
442 } else if(output_format_images == "svg") { 395 } else if(output_format_images == "svg") {
443 svg(output_heatmap_plot,width=10.5) 396 svg(output_heatmap_plot,width=10.5)
397 } else {
398 ## png(output_heatmap_plot)
399 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
400
401 bitmap(output_heatmap_plot,type="png16m",width=10.5)
444 } 402 }
445 ## else {
446 ## png(output_heatmap_plot,width=10.5)
447 ##}
448 403
449 etable2 &lt;- topTags(lrt, n=100)\$table 404 etable2 &lt;- topTags(lrt, n=100)\$table
450 order &lt;- rownames(etable2) 405 order &lt;- rownames(etable2)
451 cpm_sub &lt;- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),] 406 cpm_sub &lt;- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
452 heatmap(t(cpm_sub)) 407 heatmap(t(cpm_sub))