Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 109:dfebd3787276 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
| author | yhoogstrate |
|---|---|
| date | Tue, 01 Sep 2015 04:53:59 -0400 |
| parents | a02794bb9073 |
| children | 3112b2926266 |
| files | README.rst edgeR_Design_from_Expression_Matrix.xml edgeR_Differential_Gene_Expression.xml |
| diffstat | 3 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/README.rst Tue Sep 01 04:45:24 2015 -0400 +++ b/README.rst Tue Sep 01 04:53:59 2015 -0400 @@ -19,9 +19,11 @@ http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch -More tools by the Translational Research IT (TraIT) project can be found in the following repository: +More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: -http://toolshed.dtls.nl/ +http://toolshed.g2.bx.psu.edu + +http://testtoolshed.g2.bx.psu.edu/ License -------
--- a/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:45:24 2015 -0400 +++ b/edgeR_Design_from_Expression_Matrix.xml Tue Sep 01 04:53:59 2015 -0400 @@ -92,7 +92,6 @@ <data format="tabular" name="design_matrix" label="Design matrix" /> </outputs> - <tests> <test> <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
--- a/edgeR_Differential_Gene_Expression.xml Tue Sep 01 04:45:24 2015 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Tue Sep 01 04:53:59 2015 -0400 @@ -236,7 +236,7 @@ diff_x <- abs(max(points\$x)-min(points\$x)) - diff_y <-(max(points\$y)-min(points\$y)) + 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 logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2") points(points\$x,points\$y,pch=20) text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4) @@ -329,7 +329,7 @@ } with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance")) - with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) + with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) abline(h=c(-1,1), col="blue") dev.off() } @@ -348,8 +348,8 @@ bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14) } - expressed_genes <- subset(etable, PValue < 0.99) - h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") + expressed_genes <- subset(etable, PValue < 0.99) + h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)") center <- sum(h\$counts) / length(h\$counts) lines(c(0,1),c(center,center),lty=2,col="red",lwd=2) k <- ksmooth(h\$mid, h\$counts)