Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 3:12fb0d4b1e93 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
| author | yhoogstrate |
|---|---|
| date | Thu, 03 Sep 2015 09:42:12 -0400 |
| parents | ec951a5017f8 |
| children | 5d38abf7e4b6 |
| files | edgeR_Differential_Gene_Expression.xml |
| diffstat | 1 files changed, 88 insertions(+), 34 deletions(-) [+] |
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--- a/edgeR_Differential_Gene_Expression.xml Tue Sep 01 09:15:07 2015 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Thu Sep 03 09:42:12 2015 -0400 @@ -15,6 +15,10 @@ source="both" level="fatal" description="Have the design- and expression-matrix been swapped?" /> + <regex match="Error in eval\(expr, envir, enclos\)" + source="both" + level="fatal" + description="You have most likely used a condition in the contrast, that is not present in the Design matrix" /> <regex match="Execution halted" source="both" level="fatal" /> @@ -57,12 +61,24 @@ /dev/null #end if + #if $output_MDSplot_logFC_coordinates: + $output_MDSplot_logFC_coordinates + #else: + /dev/null + #end if + #if $output_MDSplot_bcv: $output_MDSplot_bcv #else: /dev/null #end if + #if $output_MDSplot_bcv_coordinates: + $output_MDSplot_bcv_coordinates + #else: + /dev/null + #end if + #if $output_BCVplot: $output_BCVplot #else: @@ -126,15 +142,20 @@ output_xpkm <- args[7] ##FPKM file - to be implemented output_raw_counts <- args[8] + output_MDSplot_logFC <- args[9] -output_MDSplot_bcv <- args[10] -output_BCVplot <- args[11] -output_MAplot <- args[12] -output_PValue_distribution_plot <- args[13] -output_hierarchical_clustering_plot <- args[14] -output_heatmap_plot <- args[15] -output_RData_obj <- args[16] -output_format_images <- args[17] +output_MDSplot_logFC_coordinates <- args[10] + +output_MDSplot_bcv <- args[11] +output_MDSplot_bcv_coordinates <- args[12] + +output_BCVplot <- args[13] +output_MAplot <- args[14] +output_PValue_distribution_plot <- args[15] +output_hierarchical_clustering_plot <- args[16] +output_heatmap_plot <- args[17] +output_RData_obj <- args[18] +output_format_images <- args[19] ## Obtain read-counts @@ -214,11 +235,16 @@ # hierarchical clustering makes use of the distance of the MDS - if(output_MDSplot_logFC != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") { + if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") { write("Calculating MDS plot (logFC method)",stdout()) - mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot + n_dim <- nrow(dge\$samples) + mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1)) dev.off()# Kill it + # Reset to primary dimensions + mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1] + mds_distance_logFC\$y = mds_distance_logFC\$cmdscale.out[,2] + if(output_MDSplot_logFC != "/dev/null") { write("Creating MDS plot (logFC method)",stdout()) if(output_format_images == "pdf") { @@ -236,42 +262,60 @@ diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y)) 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") points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20) - text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) + text(mds_distance_logFC\$x,mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) rm(diff_x,diff_y) dev.off() - } + } + + if(output_MDSplot_logFC_coordinates != "/dev/null") { + n_dim <- ncol(mds_distance_logFC\$cmdscale.out) + colnames(mds_distance_logFC\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_") + export <- data.frame(samples=rownames(mds_distance_logFC\$cmdscale.out),mds_distance_logFC\$cmdscale.out) + row.names(export) <- NULL + write.table(file=output_MDSplot_logFC_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE) + } } - if(output_MDSplot_bcv != "/dev/null") { + if(output_MDSplot_bcv != "/dev/null" || output_MDSplot_bcv_coordinates != "/dev/null" ) { write("Creating MDS plot (bcv method)",stdout()) ## 1. First create a virtual plot to obtain the desired coordinates - pdf("bcvmds.pdf") - mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples))) - dev.off()# Kill it + n_dim <- nrow(dge\$samples) + mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1)) + dev.off() - ## 2. Re-plot the coordinates in a new figure with the size and settings. - if(output_format_images == "pdf") { - pdf(output_MDSplot_bcv,height=14,width=14) - } else if(output_format_images == "svg") { - svg(output_MDSplot_bcv,height=14,width=14) - } else { - ## png(output_MDSplot_bcv) - ## 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/ + if(output_MDSplot_logFC != "/dev/null") { + ## 2. Re-plot the coordinates in a new figure with the size and settings. + if(output_format_images == "pdf") { + pdf(output_MDSplot_bcv,height=14,width=14) + } else if(output_format_images == "svg") { + svg(output_MDSplot_bcv,height=14,width=14) + } else { + ## png(output_MDSplot_bcv) + ## 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/ + + bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3) + } - bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3) + diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) + diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) + 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") + points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) + text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) + rm(diff_x,diff_y) + + dev.off() } - diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x)) - diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y)) - 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") - points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20) - text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) - rm(diff_x,diff_y) - - dev.off() + if(output_MDSplot_bcv_coordinates != "/dev/null") { + n_dim <- ncol(mds_distance_BCV\$cmdscale.out) + colnames(mds_distance_BCV\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_") + export <- data.frame(samples=rownames(mds_distance_BCV\$cmdscale.out),mds_distance_BCV\$cmdscale.out) + row.names(export) <- NULL + write.table(file=output_MDSplot_bcv_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE) + } } @@ -423,7 +467,9 @@ <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes"> <option value="make_output_raw_counts">Raw counts table</option> <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option> - <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; much slower)</option> + <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option> + <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; slow)</option> + <option value="make_output_MDSplot_bcv_coordinates">MDS-plot coordinates table (BCV-method; slow)</option> <option value="make_output_BCVplot">BCV-plot</option> <option value="make_output_MAplot">MA-plot</option> <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option> @@ -457,6 +503,10 @@ </change_format> </data> + <data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (logFC method)"> + <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter> + </data> + <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)"> <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter> @@ -467,6 +517,10 @@ </change_format> </data> + <data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (BCV method)"> + <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter> + </data> + <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot"> <filter>outputs and ("make_output_BCVplot" in outputs)</filter>