adjust logic around goi subsetting and re-run

AlexsLemonade · May 13, 2021 · d71f76b · d71f76b
1 parent 3ad02de
commit d71f76b
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Showing 11 changed files with 2 additions and 2 deletions.
diff --git a/analyses/oncoprint-landscape/02-plot-oncoprint.R b/analyses/oncoprint-landscape/02-plot-oncoprint.R
@@ -258,15 +258,15 @@ if (!is.null(opt$goi_list)){
   goi_list <- readr::read_tsv(opt$goi_list) %>%
     as.matrix()
 
-  maf_object <- subsetMaf(
+  filtered_maf_object <- subsetMaf(
     maf = maf_object,
     tsb = metadata$Tumor_Sample_Barcode,
     genes = goi_list,
     mafObj = TRUE
   )
 
   # Get top mutated genes per this subset object
-  gene_sum <- mafSummary(maf_object)$gene.summary
+  gene_sum <- mafSummary(filtered_maf_object)$gene.summary
 
   # Sort to get top altered genes rather than mutated only genes
   goi_list <- gene_sum %>%

diff --git a/analyses/oncoprint-landscape/plots/primary-plus_embryonal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_embryonal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_ependymal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_ependymal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_hgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_hgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_lgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_lgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_other_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_other_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_embryonal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_embryonal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_ependymal_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_ependymal_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_hgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_hgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_lgat_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_lgat_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_other_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_other_goi_oncoprint.png