Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 55:8c63794c3d3e draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Mon, 25 Aug 2014 07:36:52 -0400 |
| parents | cef8f2a174fc |
| children | d32cc25a1e13 |
| files | edgeR_Differential_Gene_Expression.xml |
| diffstat | 1 files changed, 26 insertions(+), 8 deletions(-) [+] |
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--- a/edgeR_Differential_Gene_Expression.xml Thu Jun 19 05:15:23 2014 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Mon Aug 25 07:36:52 2014 -0400 @@ -72,7 +72,9 @@ #else: /dev/null #end if - ' + + $output_format_images + ' #if $output_R: > $output_R #else: @@ -116,6 +118,12 @@ <option value="make_output_R_stdout">R stdout</option> <option value="make_output_RData_obj">R Data object</option> </param> + + <param name="output_format_images" type="select" label="Output format of images" display="radio"> + <option value="png">Portable network graphics (.png)</option> + <option value="pdf">Portable document format (.pdf)</option> + <option value="svg">Scalable vector graphics (.svg)</option> + </param> </inputs> <configfiles> @@ -146,6 +154,7 @@ output_hierarchical_clustering_plot = args[13] output_heatmap_plot = args[14] output_RData_obj = args[15] +output_format_images = args[16] library(edgeR) @@ -229,7 +238,16 @@ points <- plotMDS.DGEList(dge,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot dev.off()# Kill it - pdf(output_MDSplot) + if(output_format_images == "pdf") { + capabilities() + ##x11() + pdf(output_MDSplot) + } else if(output_format_images == "svg") { + svg(output_MDSplot) + } else { + png(output_MDSplot) + } + diff_x <- abs(max(points\$x)-min(points\$x)) diff_y <-(max(points\$y)-min(points\$y)) 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") @@ -324,27 +342,27 @@ <filter>outputs and ("make_output_raw_counts" in outputs)</filter> </data> - <data format="pdf" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot"> + <data format="${output_format_images}" name="output_MDSplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot"> <filter>outputs and ("make_output_MDSplot" in outputs)</filter> </data> - <data format="pdf" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> + <data format="${output_format_images}" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> <filter>outputs and ("make_output_BCVplot" in outputs)</filter> </data> - <data format="pdf" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot"> + <data format="${output_format_images}" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot"> <filter>outputs and ("make_output_MAplot" in outputs)</filter> </data> - <data format="pdf" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution"> + <data format="${output_format_images}" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution"> <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter> </data> - <data format="pdf" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering"> + <data format="${output_format_images}" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering"> <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter> </data> - <data format="pdf" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> + <data format="${output_format_images}" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter> </data>