| Previous changeset 8:80892c607b1e (2018-06-20) Next changeset 10:c2ac6f10b456 (2018-08-22) |
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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 80892c607b1e -r e407b1a7a8de protein_rna_correlation.r --- a/protein_rna_correlation.r Wed Jun 20 21:33:37 2018 -0400 +++ b/protein_rna_correlation.r Wed Jun 20 21:42:36 2018 -0400 |
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| @@ -638,29 +638,29 @@ file = htmloutfile, append = TRUE); outplot = paste(outdir,"/PE_GE_lm_1.png",sep="",collapse=""); - png(outplot); - #bitmap(outplot,"png16m"); + #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); - #bitmap(outplot,"png16m"); + #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); - #bitmap(outplot,"png16m"); + #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); - #bitmap(outplot,"png16m"); + #png(outplot); + bitmap(outplot,"png16m"); par(mfrow=c(1,1)); plot(regmodel, 5, cex.lab=1.5); dev.off(); @@ -711,8 +711,8 @@ cat("Generating cooksd plot\n",file=logfile, append=T); outplot = paste(outdir,"/PE_GE_lm_cooksd.png",sep="",collapse=""); - png(outplot); - #bitmap(outplot,"png16m"); + #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 @@ -772,8 +772,8 @@ # Scatter plot #============================================================================================================= outplot = paste(outdir,"/AbundancePlot_scatter_without_outliers.png",sep="",collapse=""); - png(outplot); - #bitmap(outplot,"png16m"); + #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); @@ -815,8 +815,8 @@ cat("Generating heatmap plot\n",file=logfile, append=T); outplot = paste(outdir,"/PE_GE_heatmap.png",sep="",collapse=""); - png(outplot); - #bitmap(outplot,"png16m"); + #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); @@ -837,8 +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); - #bitmap(outplot,"png16m"); + #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 80892c607b1e -r e407b1a7a8de protein_rna_correlation.xml --- a/protein_rna_correlation.xml Wed Jun 20 21:33:37 2018 -0400 +++ b/protein_rna_correlation.xml Wed Jun 20 21:42:36 2018 -0400 |
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| @@ -3,8 +3,8 @@ <requirements> <requirement type="package" version="3.2.1">R</requirement> <requirement type="package" version="0.0.1">r-protrnacorr</requirement> - <!--<requirement type="package" version="9.07">ghostscript</requirement>--> - <requirement type="package" version="1.5.0">packagelibx</requirement> + <requirement type="package" version="9.10">ghostscript</requirement> + <!--<requirement type="package" version="1.5.0">packagelibx</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 80892c607b1e -r e407b1a7a8de tool_dependencies.xml --- a/tool_dependencies.xml Wed Jun 20 21:33:37 2018 -0400 +++ b/tool_dependencies.xml Wed Jun 20 21:42:36 2018 -0400 |
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| @@ -38,10 +38,10 @@ Contains a tool dependency definition that downloads and installs protein rna correlation tool package for R library. </readme> </package> - <package name="packagelibx" version="1.5.0"> + <!--<package name="packagelibx" 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="ghostscript" version="9.10"> + <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <!--<package name="ghostscript" version="9.07"> - <repository changeset_revision="641d51248b4b" name="package_ghostscript_9_07" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package>--> </tool_dependency> |