AlexsLemonade · jaclyn-taroni · May 11, 2021 · Apr 15, 2021 · Apr 15, 2021 · Apr 22, 2021
diff --git a/analyses/oncoprint-landscape/00-map-to-sample_id.R b/analyses/oncoprint-landscape/00-map-to-sample_id.R
@@ -18,10 +18,11 @@
 #   --fusion_file ../../scratch/arriba.tsv \
 #   --metadata_file ../../data/pbta-histologies.tsv \
 #   --output_directory ../../scratch/oncoprint_files \
-#   --filename_lead "all_participants_primary_only" \
+#   --filename_lead "primary_only" \
 #   --independent_specimens ../../data/independent-specimens.wgswxs.primary.tsv
 
 library(dplyr)
+library(stringr)
 
 #### Command line options ------------------------------------------------------
 
@@ -185,8 +186,46 @@ readr::write_tsv(maf_df, maf_output)
 
 message("Preparing fusion file...")
 
+# We'll handle fusions where reciprocal fusions exist (e.g., 
+# reciprocal_exists == TRUE) separately from other fusions
+fusion_reciprocal_df <- fusion_df %>%
+  # Reciprocal fusions only
+  filter(reciprocal_exists) %>%
+  # BSID + Gene1--Gene2
+  select(Sample, FusionName) %>%
+  # Because we're only looking at presence or absence here, we can filter to 
+  # distinct identifier-fusion pairs
+  distinct() %>%
+  group_by(Sample, FusionName) %>%
+  # Put genes in the fusions in alphabetical order to collapse
+  mutate(SortedFusionName = str_c(
+    sort(str_split(FusionName,
+                   "--",
+                   simplify = TRUE),
+    ), 
+    collapse = "--")
+  ) %>%
+  ungroup() %>%
+  select(Sample,
+         FusionName = SortedFusionName) %>%
+  # When fusions are in alphabetical order, this ensures each reciprocal
+  # fusion is only counted once
+  distinct()
+
+# No need to put fusions where no reciprocal exists in alphabetical order,
+# so we handle these separately
+fusion_no_reciprocal_df <- fusion_df %>%
+  filter(!reciprocal_exists) %>%
+  select(Sample, FusionName) %>%
+  # But we can remove duplicates to avoid them being counted as multihit
+  distinct()
+
+# Bind reciprocal and no reciprocal together
+fusion_filtered_df <- bind_rows(fusion_reciprocal_df, fusion_no_reciprocal_df)
+rm(fusion_reciprocal_df, fusion_no_reciprocal_df)
+
 # Separate fusion gene partners
-fus_sep <- fusion_df %>%
+fus_sep <- fusion_filtered_df %>%
   # Separate the 5' and 3' genes
   tidyr::separate(FusionName, c("Gene1", "Gene2"), sep = "--") %>%
   # Use row numbers to mark unique fusions - this will help us when

diff --git a/analyses/oncoprint-landscape/01-plot-oncoprint.R b/analyses/oncoprint-landscape/01-plot-oncoprint.R
@@ -144,7 +144,10 @@ maf_df <- data.table::fread(opt$maf_file,
 
 # Read in cnv file
 if (!is.null(opt$cnv_file)) {
-  cnv_df <- readr::read_tsv(opt$cnv_file)
+  cnv_df <- readr::read_tsv(opt$cnv_file) %>%
+    dplyr::mutate(Variant_Classification = dplyr::case_when(Variant_Classification == "loss" ~ "Del",
+                                                            Variant_Classification %in% c("gain", "amplification") ~ "Amp",
+                                                            TRUE ~ as.character(Variant_Classification)))
 }
 
 # Read in fusion file and join

diff --git a/...ts_primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png b/...ts_primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png
diff --git a/...ipants_primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png b/...ipants_primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png
diff --git a/...landscape/plots/all_participants_primary-plus_embryonal-tumor_goi_oncoprint.png b/...landscape/plots/all_participants_primary-plus_embryonal-tumor_goi_oncoprint.png
diff --git a/...int-landscape/plots/all_participants_primary-plus_embryonal-tumor_oncoprint.png b/...int-landscape/plots/all_participants_primary-plus_embryonal-tumor_oncoprint.png
diff --git a/...landscape/plots/all_participants_primary-plus_ependymal-tumor_goi_oncoprint.png b/...landscape/plots/all_participants_primary-plus_ependymal-tumor_goi_oncoprint.png
diff --git a/...int-landscape/plots/all_participants_primary-plus_ependymal-tumor_oncoprint.png b/...int-landscape/plots/all_participants_primary-plus_ependymal-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/all_participants_primary-plus_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/all_participants_primary-plus_goi_oncoprint.png
diff --git a/...lots/all_participants_primary-plus_low-grade-astrocytic-tumor_goi_oncoprint.png b/...lots/all_participants_primary-plus_low-grade-astrocytic-tumor_goi_oncoprint.png
diff --git a/...pe/plots/all_participants_primary-plus_low-grade-astrocytic-tumor_oncoprint.png b/...pe/plots/all_participants_primary-plus_low-grade-astrocytic-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/all_participants_primary-plus_oncoprint.png b/analyses/oncoprint-landscape/plots/all_participants_primary-plus_oncoprint.png
diff --git a/...print-landscape/plots/all_participants_primary-plus_other-cns_goi_oncoprint.png b/...print-landscape/plots/all_participants_primary-plus_other-cns_goi_oncoprint.png
diff --git a/...oncoprint-landscape/plots/all_participants_primary-plus_other-cns_oncoprint.png b/...oncoprint-landscape/plots/all_participants_primary-plus_other-cns_oncoprint.png
diff --git a/...ts_primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png b/...ts_primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png
diff --git a/...ipants_primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png b/...ipants_primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png
diff --git a/...landscape/plots/all_participants_primary_only_embryonal-tumor_goi_oncoprint.png b/...landscape/plots/all_participants_primary_only_embryonal-tumor_goi_oncoprint.png
diff --git a/...int-landscape/plots/all_participants_primary_only_embryonal-tumor_oncoprint.png b/...int-landscape/plots/all_participants_primary_only_embryonal-tumor_oncoprint.png
diff --git a/...landscape/plots/all_participants_primary_only_ependymal-tumor_goi_oncoprint.png b/...landscape/plots/all_participants_primary_only_ependymal-tumor_goi_oncoprint.png
diff --git a/...int-landscape/plots/all_participants_primary_only_ependymal-tumor_oncoprint.png b/...int-landscape/plots/all_participants_primary_only_ependymal-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/all_participants_primary_only_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/all_participants_primary_only_goi_oncoprint.png
diff --git a/...lots/all_participants_primary_only_low-grade-astrocytic-tumor_goi_oncoprint.png b/...lots/all_participants_primary_only_low-grade-astrocytic-tumor_goi_oncoprint.png
diff --git a/...pe/plots/all_participants_primary_only_low-grade-astrocytic-tumor_oncoprint.png b/...pe/plots/all_participants_primary_only_low-grade-astrocytic-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/all_participants_primary_only_oncoprint.png b/analyses/oncoprint-landscape/plots/all_participants_primary_only_oncoprint.png
diff --git a/...print-landscape/plots/all_participants_primary_only_other-cns_goi_oncoprint.png b/...print-landscape/plots/all_participants_primary_only_other-cns_goi_oncoprint.png
diff --git a/...oncoprint-landscape/plots/all_participants_primary_only_other-cns_oncoprint.png b/...oncoprint-landscape/plots/all_participants_primary_only_other-cns_oncoprint.png
diff --git a/...ts/primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png b/...ts/primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png
diff --git a/.../plots/primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png b/.../plots/primary-plus_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_embryonal-tumor_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_embryonal-tumor_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_embryonal-tumor_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_embryonal-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_ependymal-tumor_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_ependymal-tumor_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_ependymal-tumor_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_ependymal-tumor_oncoprint.png
diff --git a/...print-landscape/plots/primary-plus_low-grade-astrocytic-tumor_goi_oncoprint.png b/...print-landscape/plots/primary-plus_low-grade-astrocytic-tumor_goi_oncoprint.png
diff --git a/...oncoprint-landscape/plots/primary-plus_low-grade-astrocytic-tumor_oncoprint.png b/...oncoprint-landscape/plots/primary-plus_low-grade-astrocytic-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_other-cns_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_other-cns_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary-plus_other-cns_oncoprint.png b/analyses/oncoprint-landscape/plots/primary-plus_other-cns_oncoprint.png
diff --git a/...ts/primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png b/...ts/primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_goi_oncoprint.png
diff --git a/.../plots/primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png b/.../plots/primary_only_diffuse-astrocytic-and-oligodendroglial-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_embryonal-tumor_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_embryonal-tumor_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_embryonal-tumor_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_embryonal-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_ependymal-tumor_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_ependymal-tumor_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_ependymal-tumor_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_ependymal-tumor_oncoprint.png
diff --git a/...print-landscape/plots/primary_only_low-grade-astrocytic-tumor_goi_oncoprint.png b/...print-landscape/plots/primary_only_low-grade-astrocytic-tumor_goi_oncoprint.png
diff --git a/...oncoprint-landscape/plots/primary_only_low-grade-astrocytic-tumor_oncoprint.png b/...oncoprint-landscape/plots/primary_only_low-grade-astrocytic-tumor_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_other-cns_goi_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_other-cns_goi_oncoprint.png
diff --git a/analyses/oncoprint-landscape/plots/primary_only_other-cns_oncoprint.png b/analyses/oncoprint-landscape/plots/primary_only_other-cns_oncoprint.png
diff --git a/analyses/oncoprint-landscape/run-oncoprint.sh b/analyses/oncoprint-landscape/run-oncoprint.sh
@@ -23,8 +23,8 @@ maf_consensus=../../data/pbta-snv-consensus-mutation.maf.tsv.gz
 fusion_file=../../data/pbta-fusion-putative-oncogenic.tsv
 histologies_file=../../data/pbta-histologies.tsv
 intermediate_directory=../../scratch/oncoprint_files
-primary_filename="all_participants_primary_only"
-primaryplus_filename="all_participants_primary-plus"
+primary_filename="primary_only"
+primaryplus_filename="primary-plus"
 focal_directory=../focal-cn-file-preparation/results
 focal_cnv_file=${focal_directory}/consensus_seg_most_focal_cn_status.tsv.gz
 

diff --git a/analyses/oncoprint-landscape/util/oncoplot-functions.R b/analyses/oncoprint-landscape/util/oncoplot-functions.R
@@ -71,9 +71,8 @@ prepare_maf_object <- function(maf_df,
         "Multi_Hit_Fusion",
         "Hom_Deletion",
         "Hem_Deletion",
-        "amplification",
-        "gain",
-        "loss"
+        "Amp",
+        "Del"
       )
     )
 

diff --git a/figures/palettes/oncoprint_color_palette.tsv b/figures/palettes/oncoprint_color_palette.tsv
@@ -14,8 +14,7 @@ Fusion	#7B68EE
 Multi_Hit	#CCCCCC
 Hom_Deletion	#313695
 Hem_Deletion	#abd9e9
-amplification	#c51b7d
-loss	#0072B2
-gain	#D55E00
+Del	#0072B2
+Amp	#D55E00
 High_Level_Gain	#FF0000
 Multi_Hit_Fusion	#CD96CD