Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 55:8c63794c3d3e draft

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author yhoogstrate
date Mon, 25 Aug 2014 07:36:52 -0400
parents b89788eead3c
children 25b54356ecfb
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54:cef8f2a174fc 55:8c63794c3d3e
70 #if $output_RData_obj: 70 #if $output_RData_obj:
71 $output_RData_obj 71 $output_RData_obj
72 #else: 72 #else:
73 /dev/null 73 /dev/null
74 #end if 74 #end if
75 ' 75
76 $output_format_images
77 '
76 #if $output_R: 78 #if $output_R:
77 > $output_R 79 > $output_R
78 #else: 80 #else:
79 > /dev/null 81 > /dev/null
80 #end if 82 #end if
114 <option value="make_output_heatmap_plot">Heatmap</option> 116 <option value="make_output_heatmap_plot">Heatmap</option>
115 117
116 <option value="make_output_R_stdout">R stdout</option> 118 <option value="make_output_R_stdout">R stdout</option>
117 <option value="make_output_RData_obj">R Data object</option> 119 <option value="make_output_RData_obj">R Data object</option>
118 </param> 120 </param>
121
122 <param name="output_format_images" type="select" label="Output format of images" display="radio">
123 <option value="png">Portable network graphics (.png)</option>
124 <option value="pdf">Portable document format (.pdf)</option>
125 <option value="svg">Scalable vector graphics (.svg)</option>
126 </param>
119 </inputs> 127 </inputs>
120 128
121 <configfiles> 129 <configfiles>
122 <configfile name="R_script"> 130 <configfile name="R_script">
123 library(limma,quietly=TRUE) ## enable quietly to avoid unnecessaity stderr dumping 131 library(limma,quietly=TRUE) ## enable quietly to avoid unnecessaity stderr dumping
144 output_MAplot = args[11] 152 output_MAplot = args[11]
145 output_PValue_distribution_plot = args[12] 153 output_PValue_distribution_plot = args[12]
146 output_hierarchical_clustering_plot = args[13] 154 output_hierarchical_clustering_plot = args[13]
147 output_heatmap_plot = args[14] 155 output_heatmap_plot = args[14]
148 output_RData_obj = args[15] 156 output_RData_obj = args[15]
157 output_format_images = args[16]
149 158
150 159
151 library(edgeR) 160 library(edgeR)
152 ##raw_data &lt;- read.delim(designmatrix,header=T,stringsAsFactors=T) 161 ##raw_data &lt;- read.delim(designmatrix,header=T,stringsAsFactors=T)
153 ## Obtain read-counts 162 ## Obtain read-counts
227 write("Creating MDS plot",stdout()) 236 write("Creating MDS plot",stdout())
228 ##points &lt;- plotMDS(dge,method="bcv",labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot 237 ##points &lt;- plotMDS(dge,method="bcv",labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
229 points &lt;- plotMDS.DGEList(dge,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot 238 points &lt;- plotMDS.DGEList(dge,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
230 dev.off()# Kill it 239 dev.off()# Kill it
231 240
232 pdf(output_MDSplot) 241 if(output_format_images == "pdf") {
242 capabilities()
243 ##x11()
244 pdf(output_MDSplot)
245 } else if(output_format_images == "svg") {
246 svg(output_MDSplot)
247 } else {
248 png(output_MDSplot)
249 }
250
233 diff_x &lt;- abs(max(points\$x)-min(points\$x)) 251 diff_x &lt;- abs(max(points\$x)-min(points\$x))
234 diff_y &lt;-(max(points\$y)-min(points\$y)) 252 diff_y &lt;-(max(points\$y)-min(points\$y))
235 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 MDS Plot",type="n", xlab="BCV distance 1", ylab="BCV distance 2") 253 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 MDS Plot",type="n", xlab="BCV distance 1", ylab="BCV distance 2")
236 points(points\$x,points\$y,pch=20) 254 points(points\$x,points\$y,pch=20)
237 text(points\$x, points\$y,rownames(dge\$samples),cex=0.7,col="gray",pos=4) 255 text(points\$x, points\$y,rownames(dge\$samples),cex=0.7,col="gray",pos=4)
322 340
323 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts"> 341 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
324 <filter>outputs and ("make_output_raw_counts" in outputs)</filter> 342 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
325 </data> 343 </data>
326 344
327 <data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot"> 345 <data format="${output_format_images}" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot">
328 <filter>outputs and ("make_output_MDSplot" in outputs)</filter> 346 <filter>outputs and ("make_output_MDSplot" in outputs)</filter>
329 </data> 347 </data>
330 348
331 <data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> 349 <data format="${output_format_images}" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
332 <filter>outputs and ("make_output_BCVplot" in outputs)</filter> 350 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
333 </data> 351 </data>
334 352
335 <data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot"> 353 <data format="${output_format_images}" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
336 <filter>outputs and ("make_output_MAplot" in outputs)</filter> 354 <filter>outputs and ("make_output_MAplot" in outputs)</filter>
337 </data> 355 </data>
338 356
339 <data format="pdf" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution"> 357 <data format="${output_format_images}" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
340 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter> 358 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
341 </data> 359 </data>
342 360
343 <data format="pdf" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering"> 361 <data format="${output_format_images}" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
344 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter> 362 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
345 </data> 363 </data>
346 364
347 <data format="pdf" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> 365 <data format="${output_format_images}" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
348 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter> 366 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
349 </data> 367 </data>
350 368
351 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object"> 369 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
352 <filter>outputs and ("make_output_RData_obj" in outputs)</filter> 370 <filter>outputs and ("make_output_RData_obj" in outputs)</filter>