Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison edgeR_Differential_Gene_Expression.xml @ 115:f06dceb5b966 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty
author | yhoogstrate |
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date | Tue, 01 Sep 2015 08:01:02 -0400 |
parents | 5d7efbca6c75 |
children | ed809072dc95 |
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114:5d7efbca6c75 | 115:f06dceb5b966 |
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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="3.11.0.a"> | 2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b"> |
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 <macros> | 5 <macros> |
6 <import>edgeR_macros.xml</import> | 6 <import>edgeR_macros.xml</import> |
7 </macros> | 7 </macros> |
99 /dev/null | 99 /dev/null |
100 #end if | 100 #end if |
101 | 101 |
102 $output_format_images | 102 $output_format_images |
103 ' | 103 ' |
104 #if $output_R: | |
105 > $output_R | |
106 #end if | |
107 </command> | 104 </command> |
108 | 105 |
109 <configfiles> | 106 <configfiles> |
110 <configfile name="R_script"> | 107 <configfile name="R_script"> |
111 <![CDATA[ | 108 <![CDATA[ |
236 } | 233 } |
237 | 234 |
238 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x)) | 235 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x)) |
239 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y)) | 236 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y)) |
240 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$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") | 237 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$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") |
241 mds_distance_logFC(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) | 238 points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) |
242 text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) | 239 text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) |
243 rm(diff_x,diff_y) | 240 rm(diff_x,diff_y) |
244 | 241 |
245 dev.off() | 242 dev.off() |
246 } | 243 } |
268 } | 265 } |
269 | 266 |
270 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) | 267 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) |
271 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) | 268 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) |
272 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2") | 269 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2") |
273 mds_distance_BCV(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) | 270 points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) |
274 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) | 271 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) |
275 rm(diff_x,diff_y) | 272 rm(diff_x,diff_y) |
276 | 273 |
277 dev.off() | 274 dev.off() |
278 } | 275 } |
430 <option value="make_output_BCVplot">BCV-plot</option> | 427 <option value="make_output_BCVplot">BCV-plot</option> |
431 <option value="make_output_MAplot">MA-plot</option> | 428 <option value="make_output_MAplot">MA-plot</option> |
432 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> | 429 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> |
433 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option> | 430 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option> |
434 <option value="make_output_heatmap_plot">Heatmap</option> | 431 <option value="make_output_heatmap_plot">Heatmap</option> |
435 | |
436 <option value="make_output_R_stdout">R stdout</option> | |
437 <option value="make_output_RData_obj">R Data object</option> | 432 <option value="make_output_RData_obj">R Data object</option> |
438 </param> | 433 </param> |
439 | 434 |
440 <param name="output_format_images" type="select" label="Output format of images" display="radio"> | 435 <param name="output_format_images" type="select" label="Output format of images" display="radio"> |
441 <option value="png">Portable network graphics (.png)</option> | 436 <option value="png">Portable network graphics (.png)</option> |