Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 70:fb64bf85361d draft

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author yhoogstrate
date Tue, 30 Sep 2014 10:47:33 -0400
parents 1dc20e3e11df
children e75afef75c13
comparison
equal deleted inserted replaced
69:1dc20e3e11df 70:fb64bf85361d
83 > /dev/null 83 > /dev/null
84 #end if 84 #end if
85 85
86 2> stderr.txt ; 86 2> stderr.txt ;
87 87
88 #if $output_format_images == "png": 88 #if $output_format_images.value == "png":
89 echo "Converting PDF figures to PNG" 89 echo "Converting PDF figures to PNG" ;
90 90
91 convert $output_MDSplot "{$output_MDSplot}.png" ; 91 #if $output_MDSplot:
92 convert $output_BCVplot "{$output_BCVplot}.png" ; 92 #set $output_MDSplot_tmp = str($output_MDSplot)+".png"
93 convert $output_MAplot "{$output_MAplot}.png" ; 93
94 convert $output_PValue_distribution_plot "{$output_PValue_distribution_plot}.png" ; 94 convert $output_MDSplot $output_MDSplot_tmp ;
95 convert $output_hierarchical_clustering_plot "{$output_hierarchical_clustering_plot}.png" ; 95 mv $output_MDSplot_tmp $output_MDSplot ;
96 convert $output_heatmap_plot "{$output_heatmap_plot}.png" ; 96 #end if
97 97
98 mv "{$output_MDSplot}.png" $output_MDSplot ; 98 #if $output_BCVplot:
99 mv "{$output_BCVplot}.png" $output_BCVplot ; 99 #set $output_BCVplot_tmp = str($output_BCVplot)+".png"
100 mv "{$output_MAplot}.png" $output_MAplot ; 100
101 mv "{$output_PValue_distribution_plot}.png" $output_PValue_distribution_plot ; 101 convert $output_BCVplot $output_BCVplot_tmp ;
102 mv "{$output_hierarchical_clustering_plot}.png" $output_hierarchical_clustering_plot ; 102 mv $output_BCVplot_tmp $output_BCVplot ;
103 mv "{$output_heatmap_plot}.png" $output_heatmap_plot ; 103 #end if
104 104
105 mv "{$output_format_images}.png" $output_format_images ; 105 #if $output_MAplot:
106 #else: 106 #set $output_MAplot_tmp = str($output_MAplot)+".png"
107 echo "Format is already in $output_format_images" 107
108 convert $output_MAplot $output_MAplot_tmp ;
109 mv $output_MAplot_tmp $output_MAplot ;
110 #end if
111
112 #if $output_PValue_distribution_plot:
113 #set $output_PValue_distribution_plot_tmp = str($output_PValue_distribution_plot)+".png"
114
115 convert $output_PValue_distribution_plot $output_PValue_distribution_plot_tmp ;
116 mv $output_PValue_distribution_plot_tmp $output_PValue_distribution_plot ;
117 #end if
118
119 #if $output_hierarchical_clustering_plot:
120 #set $output_hierarchical_clustering_plot_tmp = str($output_hierarchical_clustering_plot)+".png"
121
122 convert $output_hierarchical_clustering_plot $output_hierarchical_clustering_plot_tmp ;
123 mv $output_hierarchical_clustering_plot_tmp $output_hierarchical_clustering_plot ;
124 #end if
125
126 #if $output_heatmap_plot:
127 #set $output_heatmap_plot_tmp = str($output_heatmap_plot)+".png"
128
129 convert $output_heatmap_plot $output_heatmap_plot_tmp ;
130 mv $output_heatmap_plot_tmp $output_heatmap_plot ;
131 #end if
108 #end if 132 #end if
109 133
110 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 134 grep -v 'Calculating library sizes from column' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ;
111 135
112 ## Locale error messages: 136 ## Locale error messages:
264 288
265 if(output_format_images == "pdf" || output_format_images == "png") { 289 if(output_format_images == "pdf" || output_format_images == "png") {
266 pdf(output_MDSplot) 290 pdf(output_MDSplot)
267 } else if(output_format_images == "svg") { 291 } else if(output_format_images == "svg") {
268 svg(output_MDSplot) 292 svg(output_MDSplot)
269 ##} else { 293 }
294 ## else {
270 ## png(output_MDSplot) 295 ## png(output_MDSplot)
271 ##} 296 ##}
272 297
273 diff_x <- abs(max(points\$x)-min(points\$x)) 298 diff_x <- abs(max(points\$x)-min(points\$x))
274 diff_y <-(max(points\$y)-min(points\$y)) 299 diff_y <-(max(points\$y)-min(points\$y))
285 310
286 if(output_format_images == "pdf" || output_format_images == "png") { 311 if(output_format_images == "pdf" || output_format_images == "png") {
287 pdf(output_BCVplot) 312 pdf(output_BCVplot)
288 } else if(output_format_images == "svg") { 313 } else if(output_format_images == "svg") {
289 svg(output_BCVplot) 314 svg(output_BCVplot)
290 ##} else { 315 }
316 ##else {
291 ## png(output_BCVplot) 317 ## png(output_BCVplot)
292 ##} 318 ##}
293 319
294 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance") 320 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
295 dev.off() 321 dev.off()
320 346
321 if(output_format_images == "pdf" || output_format_images == "png") { 347 if(output_format_images == "pdf" || output_format_images == "png") {
322 pdf(output_MAplot) 348 pdf(output_MAplot)
323 } else if(output_format_images == "svg") { 349 } else if(output_format_images == "svg") {
324 svg(output_MAplot) 350 svg(output_MAplot)
325 ##} else { 351 }
352 ##else {
326 ## png(output_MAplot) 353 ## png(output_MAplot)
327 ##} 354 ##}
328 355
329 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) 356 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
330 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) 357 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
337 364
338 if(output_format_images == "pdf" || output_format_images == "png") { 365 if(output_format_images == "pdf" || output_format_images == "png") {
339 pdf(output_PValue_distribution_plot) 366 pdf(output_PValue_distribution_plot)
340 } else if(output_format_images == "svg") { 367 } else if(output_format_images == "svg") {
341 svg(output_PValue_distribution_plot) 368 svg(output_PValue_distribution_plot)
342 ##} else { 369 }
370 ##else {
343 ## png(output_PValue_distribution_plot) 371 ## png(output_PValue_distribution_plot)
344 ##} 372 ##}
345 373
346 expressed_genes <- subset(etable, PValue < 0.99) 374 expressed_genes <- subset(etable, PValue < 0.99)
347 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") 375 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
363 391
364 if(output_format_images == "pdf" || output_format_images == "png") { 392 if(output_format_images == "pdf" || output_format_images == "png") {
365 pdf(output_heatmap_plot,width=10.5) 393 pdf(output_heatmap_plot,width=10.5)
366 } else if(output_format_images == "svg") { 394 } else if(output_format_images == "svg") {
367 svg(output_heatmap_plot,width=10.5) 395 svg(output_heatmap_plot,width=10.5)
368 ##} else { 396 }
397 ## else {
369 ## png(output_heatmap_plot,width=10.5) 398 ## png(output_heatmap_plot,width=10.5)
370 ##} 399 ##}
371 400
372 etable2 <- topTags(lrt, n=100)\$table 401 etable2 <- topTags(lrt, n=100)\$table
373 order <- rownames(etable2) 402 order <- rownames(etable2)