| Previous changeset 5:6bf0203ee17e (2018-06-20) Next changeset 7:fdd5707c6127 (2018-06-20) |
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Commit message:
planemo upload |
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modified:
protein_rna_correlation.r protein_rna_correlation.xml tool_dependencies.xml |
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| diff -r 6bf0203ee17e -r 8e9428eca82c protein_rna_correlation.r --- a/protein_rna_correlation.r Wed Jun 20 20:43:56 2018 -0400 +++ b/protein_rna_correlation.r Wed Jun 20 21:09:54 2018 -0400 |
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| @@ -536,7 +536,8 @@ #============================================================================================================= cat("Generating Box and Density plot\n",file=logfile, append=T); outplot = paste(outdir,"/AbundancePlot.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot, "png16m"); par(mfrow=c(2,2)); boxplot(proteome_df[,2], ylab="Abundance", main="Proteome abundance", cex.lab=1.5); plot(density(proteome_df[,2]), xlab="Protein Abundance", ylab="Density", main="Proteome abundance", cex.lab=1.5); @@ -554,7 +555,8 @@ #============================================================================================================= cat("Generating scatter plot\n",file=logfile, append=T); outplot = paste(outdir,"/AbundancePlot_scatter.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m") par(mfrow=c(1,1)); scatter.smooth(transcriptome_df[,2], proteome_df[,2], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5); @@ -636,25 +638,29 @@ file = htmloutfile, append = TRUE); outplot = paste(outdir,"/PE_GE_lm_1.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(regmodel, 1, cex.lab=1.5); dev.off(); outplot = paste(outdir,"/PE_GE_lm_2.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(regmodel, 2, cex.lab=1.5); dev.off(); outplot = paste(outdir,"/PE_GE_lm_3.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(regmodel, 3, cex.lab=1.5); dev.off(); outplot = paste(outdir,"/PE_GE_lm_5.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(regmodel, 5, cex.lab=1.5); dev.off(); @@ -705,7 +711,8 @@ cat("Generating cooksd plot\n",file=logfile, append=T); outplot = paste(outdir,"/PE_GE_lm_cooksd.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(cooksd, pch="*", cex=2, cex.lab=1.5,main="Influential Obs. by Cooks distance", ylab="Cook\'s distance", xlab="Observations") # plot cooks distance abline(h = 4*mean(cooksd, na.rm=T), col="red") # add cutoff line @@ -765,7 +772,8 @@ # Scatter plot #============================================================================================================= outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); scatter.smooth(PE_GE_data_no_outlier[,"GE_abundance"], PE_GE_data_no_outlier[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5); @@ -807,7 +815,8 @@ cat("Generating heatmap plot\n",file=logfile, append=T); outplot = paste(outdir,"/PE_GE_heatmap.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); #heatmap.2(as.matrix(PE_GE_data[,c("PE_abundance","GE_abundance")]), trace="none", cexCol=1, col=greenred(100),Colv=F, labCol=c("PE","GE"), scale="col"); my_palette <- colorRampPalette(c("green", "white", "red"))(299); @@ -828,7 +837,8 @@ k1 = kmeans(PE_GE_data_kdata[,c("PE_abundance","GE_abundance")], 5); cat("Generating kmeans plot\n",file=logfile, append=T); outplot = paste(outdir,"/PE_GE_kmeans.png",sep="",collapse=""); - png(outplot); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); scatter.smooth(PE_GE_data_kdata[,"GE_abundance"], PE_GE_data_kdata[,"PE_abundance"], xlab="Transcript Abundance", ylab="Protein Abundance", cex.lab=1.5); |
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| diff -r 6bf0203ee17e -r 8e9428eca82c protein_rna_correlation.xml --- a/protein_rna_correlation.xml Wed Jun 20 20:43:56 2018 -0400 +++ b/protein_rna_correlation.xml Wed Jun 20 21:09:54 2018 -0400 |
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| @@ -3,8 +3,7 @@ <requirements> <requirement type="package" version="3.2.1">R</requirement> <requirement type="package" version="0.0.1">r-protrnacorr</requirement> - <requirement type="package" version="1.5.0">x11</requirement> - + <!--<requirement type="package" version="1.5.0">x11</requirement>--> </requirements> <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[protein_rna_correlation.r $pe_exp $ge_exp $pe_idcol $ge_idcol $pe_expcol $ge_expcol $pe_idtype $ge_idtype $organism_map $writeMapUnmap $doScale $html_file $html_file.files_path]]></command> <inputs> |
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| diff -r 6bf0203ee17e -r 8e9428eca82c tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 20 20:43:56 2018 -0400 +++ b/tool_dependencies.xml Wed Jun 20 21:09:54 2018 -0400 |
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| @@ -38,7 +38,7 @@ Contains a tool dependency definition that downloads and installs protein rna correlation tool package for R library. </readme> </package> - <package name="x11" version="1.5.0"> - <repository changeset_revision="2ecb3f1f8fbb" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> + <!--<package name="x11" version="1.5.0"> + <repository changeset_revision="2ecb3f1f8fbb" name="package_libx11_1_5_0" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package>--> </tool_dependency> |