# HG changeset patch # User morinlab # Date 1473708696 14400 # Node ID 97767a410c75e900090909bcf92821a4b8f0bf48 Uploaded diff -r 000000000000 -r 97767a410c75 oncoprintplus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/oncoprintplus.xml Mon Sep 12 15:31:36 2016 -0400 @@ -0,0 +1,161 @@ + + + + creates a summary matrix plot of cohort wide mutations + + + + Rscript + R + cancer_genomics_functions + CANCER_GENOMICS_FUNCTIONS_PATH + boutroslab_plotting_general + + + + + touch output.pdf; + Rscript $__tool_directory__/oncoprintplus.R + --input_snv $input_maf + --cancer_genomics_functions_path \$CANCER_GENOMICS_FUNCTIONS_PATH/ + + #if $gene.order.value == "default" + + #else + --gene_order $gene.order + #end if + + #if $gene.gene_list + --gene_list $gene.gene_list + #end if + + #if $gene.snv_counts + --plot_gene_snv_counts + #end if + + #if $gene.mutsig.plot + --plot_gene_mutsig + #end if + + #if $gene.mutsig.mutsig + --gene_mutsig $gene.mutsig.mutsig + #end if + + #if $gene.oncodrive.plot + --plot_gene_oncodrive + #end if + + #if $gene.oncodrive.oncodrive + --gene_oncodrive $gene.oncodrive.oncodrive + #end if + + #if $patient.covariates.use_covariates == "no": + + #if $patient.covariates.order.value == "default": + + #else + --patient_order snv_counts + #end if + + #else + + --patient_covariate_data $patient.covariates.covariate_data + + #for $item in $patient.covariates.plot: + --plot_patient_covariate $item.covariate_to_plot + #end for + + #for $item in $patient.covariates.order: + --patient_order $item.covariate_or_internal.order + #end for + + #end if + + #if $patient.snv_counts + --plot_patient_snv_counts + #end if + + #if $patient.snv_distribution + --plot_patient_snv_distribution + #end if + + --center_plot $center_plot + --output ./output.pdf; + + mv output.pdf $output; + + + + + + + + + + + + +
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