From 78220da9026c4c2d2e17e14ecbe6be6dfd57a37f Mon Sep 17 00:00:00 2001
From: runjin326 <47674661+runjin326@users.noreply.github.com>
Date: Fri, 22 Oct 2021 20:21:18 -0400
Subject: [PATCH] Oncoprint output count tables  (#1191)

---
 .../oncoprint-landscape/01-map-to-sample_id.R |   2 +-
 .../oncoprint-landscape/02-plot-oncoprint.R   |  26 +-
 .../03-oncoprint-n-count-table.R              | 236 ++++++++++++++++++
 analyses/oncoprint-landscape/README.md        |   8 +-
 analyses/oncoprint-landscape/run-oncoprint.sh |  22 +-
 ...ary-plus_embryonal_oncoprint_summary_n.tsv |  48 ++++
 .../primary-plus_hgat_oncoprint_summary_n.tsv |  84 +++++++
 .../primary-plus_lgat_oncoprint_summary_n.tsv |  23 ++
 .../primary-plus_n_per_cancer_group.tsv       |   0
 ...primary-plus_other_oncoprint_summary_n.tsv |  44 ++++
 ...ary_only_embryonal_oncoprint_summary_n.tsv |  45 ++++
 .../primary_only_hgat_oncoprint_summary_n.tsv |  82 ++++++
 .../primary_only_lgat_oncoprint_summary_n.tsv |  23 ++
 .../primary_only_n_per_cancer_group.tsv       |   0
 ...primary_only_other_oncoprint_summary_n.tsv |  40 +++
 .../tables/sample_n_in_oncoprint.tsv          |   9 +
 16 files changed, 681 insertions(+), 11 deletions(-)
 create mode 100644 analyses/oncoprint-landscape/03-oncoprint-n-count-table.R
 create mode 100644 analyses/oncoprint-landscape/tables/primary-plus_embryonal_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/primary-plus_hgat_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/primary-plus_lgat_oncoprint_summary_n.tsv
 rename analyses/oncoprint-landscape/{data => tables}/primary-plus_n_per_cancer_group.tsv (100%)
 create mode 100644 analyses/oncoprint-landscape/tables/primary-plus_other_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/primary_only_embryonal_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/primary_only_hgat_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/primary_only_lgat_oncoprint_summary_n.tsv
 rename analyses/oncoprint-landscape/{data => tables}/primary_only_n_per_cancer_group.tsv (100%)
 create mode 100644 analyses/oncoprint-landscape/tables/primary_only_other_oncoprint_summary_n.tsv
 create mode 100644 analyses/oncoprint-landscape/tables/sample_n_in_oncoprint.tsv

diff --git a/analyses/oncoprint-landscape/01-map-to-sample_id.R b/analyses/oncoprint-landscape/01-map-to-sample_id.R
index f66d0ba3ff..27da3630e7 100644
--- a/analyses/oncoprint-landscape/01-map-to-sample_id.R
+++ b/analyses/oncoprint-landscape/01-map-to-sample_id.R
@@ -387,7 +387,7 @@ gather_n_per_cancer_group <- function(metadata, broad_histology){
   }
 }
 
-output_file <- file.path('data', paste0(opt$filename_lead, "_n_per_cancer_group.tsv"))
+output_file <- file.path('tables', paste0(opt$filename_lead, "_n_per_cancer_group.tsv"))
 lapply(as.list(c("Low-grade astrocytic tumor","Embryonal tumor",
          "Diffuse astrocytic and oligodendroglial tumor",
          "Other CNS")), function(x) gather_n_per_cancer_group(histologies_df,x)) %>%
diff --git a/analyses/oncoprint-landscape/02-plot-oncoprint.R b/analyses/oncoprint-landscape/02-plot-oncoprint.R
index f6ee9bdf87..8d21c34e38 100644
--- a/analyses/oncoprint-landscape/02-plot-oncoprint.R
+++ b/analyses/oncoprint-landscape/02-plot-oncoprint.R
@@ -43,6 +43,14 @@ if (!dir.exists(plots_dir)) {
   dir.create(plots_dir)
 }
 
+# Path to output directory for tables produced
+tables_dir <-
+  file.path(root_dir, "analyses", "oncoprint-landscape", "tables")
+
+if (!dir.exists(tables_dir)) {
+  dir.create(tables_dir)
+}
+
 # Source the custom functions script
 source(
   file.path(
@@ -112,6 +120,12 @@ option_list <- list(
     action = "store_true",
     default = FALSE,
     help = "logical statement on whether to include intronic variants in oncoprint plot"
+  ),
+  optparse::make_option(
+    c("--output_table"),
+    type = "character",
+    default = NULL,
+    help = "file name for the output tables"
   )
 )
 
@@ -269,22 +283,26 @@ if (!is.null(opt$goi_list)){
   # Get top mutated genes per this subset object
   gene_sum <- mafSummary(filtered_maf_object)$gene.summary
   
+  # write out results 
+  if (!is.null(opt$output_table)) {
+    readr::write_tsv(gene_sum, file.path("tables", opt$output_table))
+  }
+  
   # Sort to get top altered genes rather than mutated only genes
   goi_list <- gene_sum %>%
     dplyr::arrange(dplyr::desc(AlteredSamples)) %>%
     # Filter to genes where multiple samples have an alteration
     dplyr::filter(AlteredSamples > 1) %>%
     dplyr::pull(Hugo_Symbol)
-  
+
   if (opt$top_n < length(goi_list)) {
     # Now let's filter to the `top_n` genes
     goi_list <- goi_list[1:opt$top_n]
-    
+
   }
-  
 }
 
-#### Plot and Save Oncoprint --------------------------------------------------
+### Plot and Save Oncoprint --------------------------------------------------
 
 # Given a maf object, plot an oncoprint of the variants in the
 # dataset and save as a png file.
diff --git a/analyses/oncoprint-landscape/03-oncoprint-n-count-table.R b/analyses/oncoprint-landscape/03-oncoprint-n-count-table.R
new file mode 100644
index 0000000000..082bdf7355
--- /dev/null
+++ b/analyses/oncoprint-landscape/03-oncoprint-n-count-table.R
@@ -0,0 +1,236 @@
+# This script outputs the oncoprint N counts table 
+
+#### Set Up --------------------------------------------------------------------
+
+# Load libraries
+library(dplyr)
+library(maftools)
+
+# Get `magrittr` pipe
+`%>%` <- dplyr::`%>%`
+
+#### Directories and Files -----------------------------------------------------
+
+# Detect the ".git" folder -- this will in the project root directory.
+# Use this as the root directory to ensure proper execution, no matter where
+# it is called from.
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+# Path to output directory for table produced
+results_dir <-
+  file.path(root_dir, "analyses", "oncoprint-landscape", "tables")
+
+if (!dir.exists(results_dir)) {
+  dir.create(results_dir)
+}
+
+#### Command line options ------------------------------------------------------
+
+# Declare command line options
+option_list <- list(
+  optparse::make_option(
+    c("-m", "--maf_file_po"),
+    type = "character",
+    default = NULL,
+    help = "file path to MAF file that contains SNV information of primary_only samples",
+  ),
+  optparse::make_option(
+    c("-c", "--cnv_file_po"),
+    type = "character",
+    default = NULL,
+    help = "file path to file that contains CNV information of primary_only samples"
+  ),
+  optparse::make_option(
+    c("-f", "--fusion_file_po"),
+    type = "character",
+    default = NULL,
+    help = "file path to file that contains fusion information of primary_only samples"
+  ),
+  optparse::make_option(
+    c("-g", "--maf_file_pp"),
+    type = "character",
+    default = NULL,
+    help = "file path to MAF file that contains SNV information of primary-plus samples",
+  ),
+  optparse::make_option(
+    c("-d", "--cnv_file_pp"),
+    type = "character",
+    default = NULL,
+    help = "file path to file that contains CNV information of primary-plus samples"
+  ),
+  optparse::make_option(
+    c("-e", "--fusion_file_pp"),
+    type = "character",
+    default = NULL,
+    help = "file path to file that contains fusion information of primary-plus samples"
+  ),
+  optparse::make_option(
+    c("-s", "--metadata_file"),
+    type = "character",
+    default = NULL,
+    help = "file path to the histologies file"
+  ),
+  optparse::make_option(
+    c("-l", "--goi_list"),
+    type = "character",
+    default = NULL,
+    help = "comma-separated list of genes of interest files that contain the
+            genes to include on oncoprint"
+  ),
+  optparse::make_option(
+    c("-b", "--broad_histology_list"),
+    type = "character",
+    default = NULL,
+    help = "comma-separated list of `broad_histology` value to output numbers entering oncoprint"
+  ),
+  optparse::make_option(
+    c("-o", "--short_name_list"),
+    type = "character",
+    default = NULL,
+    help = "comma-separated list of file prefix for output tables"
+  ),
+  optparse::make_option(
+    c("--include_introns"),
+    action = "store_true",
+    default = FALSE,
+    help = "logical statement on whether to include intronic variants in oncoprint plot"
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+# Define cnv_file, fusion_file, and genes object here as they still need to
+# be defined for the `prepare_and_plot_oncoprint` custom function (the
+# cnv_file specifically for the `read.maf` function within the custom function),
+# even if they are NULL
+broad_histology_list<-unlist(strsplit(opt$broad_histology_list,","))
+short_name_list<-unlist(strsplit(opt$short_name_list,","))
+
+# Source the custom functions script
+source(
+  file.path(
+    root_dir,
+    "analyses",
+    "oncoprint-landscape",
+    "util",
+    "oncoplot-functions.R"
+  )
+)
+
+#### Read in data --------------------------------------------------------------
+
+# Read in metadata
+metadata <- readr::read_tsv(opt$metadata_file, guess_max = 10000) %>%
+  dplyr::rename(Tumor_Sample_Barcode = sample_id)
+
+# Read in MAF file
+maf_df_po <- data.table::fread(opt$maf_file_po,
+                               stringsAsFactors = FALSE,
+                               data.table = FALSE)
+maf_df_pp <- data.table::fread(opt$maf_file_pp,
+                               stringsAsFactors = FALSE,
+                               data.table = FALSE)
+
+if (!opt$include_introns) {
+  maf_df_po <- maf_df_po %>%
+    dplyr::filter(Variant_Classification != "Intron")
+  
+  maf_df_pp <- maf_df_pp %>%
+    dplyr::filter(Variant_Classification != "Intron")
+}
+
+# Read in cnv file
+cnv_df_po <- readr::read_tsv(opt$cnv_file_po) 
+cnv_df_pp <- readr::read_tsv(opt$cnv_file_pp) 
+
+
+# Read in fusion file and join
+fusion_df_po <- readr::read_tsv(opt$fusion_file_po)
+fusion_df_pp <- readr::read_tsv(opt$fusion_file_pp)
+
+
+#### Set up oncoprint annotation objects --------------------------------------
+oncoprint_n_table_po <- data.frame(matrix(ncol = 3, nrow = 0))
+oncoprint_n_table_pp <- data.frame(matrix(ncol = 3, nrow = 0))
+
+colnames(oncoprint_n_table_po) <- c("broad_histology", "n_sample", "tumor_type")
+colnames(oncoprint_n_table_pp) <- c("broad_histology", "n_sample", "tumor_type")
+
+for(i in 1:length(broad_histology_list)){
+  histology_of_interest <- broad_histology_list[i]
+  
+  if (!histology_of_interest == "Other CNS") {
+    metadata_each <- metadata %>%
+      dplyr::filter(broad_histology == histology_of_interest)
+  } else {
+    metadata_each <- metadata %>%
+      dplyr::filter(
+        broad_histology %in% c(
+          "Ependymal tumor",
+          "Tumors of sellar region",
+          "Neuronal and mixed neuronal-glial tumor",
+          "Tumor of cranial and paraspinal nerves",
+          "Meningioma",
+          "Mesenchymal non-meningothelial tumor",
+          "Germ cell tumor",
+          "Choroid plexus tumor",
+          "Histiocytic tumor",
+          "Tumor of pineal region",
+          "Metastatic tumors",
+          "Other astrocytic tumor",
+          "Lymphoma",
+          "Melanocytic tumor",
+          "Other tumor"
+        )
+      )
+    }
+  # Now filter the remaining data files
+  maf_po_each <- maf_df_po %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  cnv_po_each <- cnv_df_po %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  fusion_po_each <- fusion_df_po %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  # get bs ids in each dataframe
+  maf_po_bsid <- maf_po_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  cnv_po_bsid <- cnv_po_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  fusion_po_bsid <- fusion_po_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  # take union
+  all_po_bsid <- union(maf_po_bsid, cnv_po_bsid) %>% union(fusion_po_bsid) 
+  # write out broad histology and number of samples to a table 
+  oncoprint_n_table_po[i,1] <- histology_of_interest
+  oncoprint_n_table_po[i,2] <- length(all_po_bsid)
+  oncoprint_n_table_po[i,3] <- "primary_only"
+  
+  # Now do the same thing for primary plus samples
+  maf_pp_each <- maf_df_pp %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  cnv_pp_each <- cnv_df_pp %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  fusion_pp_each <- fusion_df_pp %>%
+    dplyr::filter(Tumor_Sample_Barcode %in% metadata_each$Tumor_Sample_Barcode)
+  
+  # get bs ids in each dataframe
+  maf_pp_bsid <- maf_pp_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  cnv_pp_bsid <- cnv_pp_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  fusion_pp_bsid <- fusion_pp_each %>% pull(Tumor_Sample_Barcode) %>% unique()
+  # take union
+  all_pp_bsid <- union(maf_pp_bsid, cnv_pp_bsid) %>% union(fusion_pp_bsid) 
+  # write out broad histology and number of samples to a table 
+  oncoprint_n_table_pp[i,1] <- histology_of_interest
+  oncoprint_n_table_pp[i,2] <- length(all_pp_bsid)
+  oncoprint_n_table_pp[i,3] <- "primary-plus"
+  
+}
+
+# write out n number entering oncoprint
+bind_rows(oncoprint_n_table_pp, oncoprint_n_table_po) %>% 
+  readr::write_tsv(file.path(results_dir, "sample_n_in_oncoprint.tsv"))
+
diff --git a/analyses/oncoprint-landscape/README.md b/analyses/oncoprint-landscape/README.md
index e0df5754fa..613c0ab778 100644
--- a/analyses/oncoprint-landscape/README.md
+++ b/analyses/oncoprint-landscape/README.md
@@ -22,7 +22,8 @@ bash run-oncoprint.sh
   * Filtering via an [independent specimen file](https://alexslemonade.github.io/OpenPBTA-manuscript/#selection-of-independent-samples) is optional, but highly recommended.
 * `02-plot-oncoprint.R` takes the files from above and optionally a file or set of files (to be concatenated) that will restrict the set of genes that are being plotted in an OncoPrint.
 	* Running this via `run-oncoprint.sh` will restrict plotting to a list of top mutated genes (generated in `analyses/interaction-plots/scripts/01-disease-specimen-lists.R`) and top genes with recurrent CNVs (generated in `analyses/focal-cn-file-preparation/06-find-recurrent-calls.Rmd`)
-
+  * This script also returns tables summary of the total of number of samples that have alterations in gene of interest
+* `03-oncoprint-n-count-table.R` counts the number of samples that enter oncoprint plotting (with or without alterations in genes of interest) for each broad histology group
 
 ### Folder Structure
 
@@ -30,6 +31,7 @@ bash run-oncoprint.sh
 ├── 00-prepare-goi-lists.R
 ├── 01-map-to-sample_id.R
 ├── 02-plot-oncoprint.R
+├── 03-oncoprint-n-count-table.R
 ├── README.md
 ├── data
 │   ├── embryonal-tumor_goi_list.tsv
@@ -45,6 +47,10 @@ bash run-oncoprint.sh
 │   ├── primary-plus_*histology*_oncoprint.png
 │   ├── primary_only_*histology*_goi_oncoprint.png
 │   └── primary_only_*histology*_oncoprint.png
+├── tables
+│   ├── summary_n_in_oncoprint.tsv
+│   ├── primary-plus_*histology*_summary_n.tsv
+│   └── primary_only_*histology*_summary_n.tsv
 ├── run-oncoprint.sh
 └── util
     └── oncoplot-functions.R
diff --git a/analyses/oncoprint-landscape/run-oncoprint.sh b/analyses/oncoprint-landscape/run-oncoprint.sh
index aa428f58fb..0dea397684 100644
--- a/analyses/oncoprint-landscape/run-oncoprint.sh
+++ b/analyses/oncoprint-landscape/run-oncoprint.sh
@@ -74,7 +74,7 @@ declare -A labels=(
 )
 
 declare -A goi_files=(
-  [lgat]="lgat_goi_list.tsv"  
+  [lgat]="lgat_goi_list.tsv"
   [embryonal]="embryonal-tumor_goi_list.tsv"
   [hgat]="hgat_goi_list.tsv"
   [other]="other_goi_list.tsv"
@@ -94,8 +94,8 @@ for histology in "${histologies[@]}"; do
       --fusion_file "${intermediate_directory}/${filename}_fusions.tsv" \
       --metadata_file "${histologies_file}" \
       --png_name "${filename}_${histology}_oncoprint.png" \
-      --broad_histology "${labels[$histology]}"
-      
+      --broad_histology "${labels[$histology]}" 
+
     # Genes of interest only version of oncoprint
     Rscript --vanilla 02-plot-oncoprint.R \
       --maf_file "${intermediate_directory}/${filename}_maf.tsv" \
@@ -105,7 +105,19 @@ for histology in "${histologies[@]}"; do
       --goi_list "${oncoprint_data_directory}/${goi_files[$histology]}" \
       --top_n 20 \
       --png_name "${filename}_${histology}_goi_oncoprint.png" \
-      --broad_histology "${labels[$histology]}"
+      --broad_histology "${labels[$histology]}" \
+      --output_table "${filename}_${histology}_oncoprint_summary_n.tsv"
 
-  done  
+  done
 done
+
+Rscript --vanilla 03-oncoprint-n-count-table.R \
+  --maf_file_po "${intermediate_directory}/primary_only_maf.tsv" \
+  --cnv_file_po "${intermediate_directory}/primary_only_cnv.tsv" \
+  --fusion_file_po "${intermediate_directory}/primary_only_fusions.tsv" \
+  --maf_file_pp "${intermediate_directory}/primary-plus_maf.tsv" \
+  --cnv_file_pp "${intermediate_directory}/primary-plus_cnv.tsv" \
+  --fusion_file_pp "${intermediate_directory}/primary-plus_fusions.tsv" \
+  --metadata_file "${histologies_file}" \
+  --broad_histology_list "Low-grade astrocytic tumor,Embryonal tumor,Diffuse astrocytic and oligodendroglial tumor,Other CNS" \
+  --short_name_list "lgat,embryonal,hgat,other" 
diff --git a/analyses/oncoprint-landscape/tables/primary-plus_embryonal_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary-plus_embryonal_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..81107ab5c5
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary-plus_embryonal_oncoprint_summary_n.tsv
@@ -0,0 +1,48 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	Splice_Region	Silent	RNA	5'UTR	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+CTNNB1	0	0	0	0	1	0	12	0	0	0	0	0	0	0	0	13	0	0	0	13	13
+DDX3X	1	0	0	0	0	1	7	0	1	1	1	0	0	0	1	13	0	0	0	12	12
+TP53	0	0	1	0	0	0	6	0	1	2	1	0	0	0	0	11	0	0	0	9	9
+KMT2C	0	0	2	2	0	0	2	0	1	0	2	0	1	0	0	10	0	0	0	9	9
+KDM6A	1	0	0	1	0	0	0	0	2	3	1	1	0	0	0	9	0	0	0	9	9
+KMT2D	0	0	2	2	0	0	1	0	3	1	0	0	0	0	0	9	0	0	0	8	8
+SMARCA4	0	1	0	0	0	0	7	0	0	0	0	0	0	0	0	8	0	0	0	6	6
+PTCH1	0	1	3	1	0	0	0	0	0	1	1	0	0	0	0	7	0	0	0	6	6
+TERT	0	4	0	0	0	0	0	0	0	0	0	1	0	0	0	5	1	0	1	4	5
+KSR2	0	1	0	0	0	0	0	0	0	0	3	0	0	0	0	4	0	0	0	4	4
+ATM	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	3	0	0	0	3	3
+CDK6	0	1	0	0	0	0	0	0	0	0	2	0	0	0	0	3	0	0	0	3	3
+IGFN1	1	0	0	0	0	0	1	0	0	0	0	0	1	0	0	3	0	0	0	3	3
+TCF4	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	3	0	0	0	3	3
+TTYH1	0	0	0	0	2	0	0	1	0	0	0	0	0	0	0	3	3	0	3	3	3
+ZIC1	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	3	0	0	0	3	3
+ZMYM3	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	3	0	0	0	3	3
+APC	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	2	0	0	0	2	2
+CREBBP	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	2	2
+CTDNEP1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	2	2
+FOXO3	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	0	0	0	2	2
+GSE1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+KBTBD4	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+MIR17HG	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	2	2
+PRKAR1A	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	2	1	0	1	2	3
+PTEN	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	2	0	0	0	1	1
+ARID1A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+BCOR	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CENPE	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+DICER1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+DYNC2H1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+FOXR2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+MED12	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1
+MIR512-2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	3	0	3	1	4
+MSH2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+MYCN	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	2	0	2	1	3
+OTX2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+PIK3CA	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+SNCAIP	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+SUFU	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	1	1	2
+TBR1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+IDH1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
+MIR1323	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	3
+MIR515-2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	3
+MIR519C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	3	0	3
+SMARCB1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2
+TFPT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2
diff --git a/analyses/oncoprint-landscape/tables/primary-plus_hgat_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary-plus_hgat_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..a604212042
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary-plus_hgat_oncoprint_summary_n.tsv
@@ -0,0 +1,84 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Del	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	Silent	Splice_Region	5'UTR	RNA	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+TP53	6	0	2	0	0	1	0	42	0	7	2	1	2	1	0	0	64	0	0	0	44	44
+H3F3A	0	1	0	0	0	0	0	40	0	0	0	0	0	0	0	0	41	0	0	0	41	41
+ATRX	0	1	7	2	2	0	0	14	0	3	2	2	1	0	0	0	34	0	2	2	23	24
+NF1	1	2	8	2	1	0	0	4	0	8	2	2	1	0	0	0	31	0	0	0	17	17
+PIK3CA	0	1	0	0	0	4	0	9	0	0	0	4	0	0	0	0	18	0	0	0	14	14
+EGFR	1	0	0	0	1	0	1	14	0	0	0	5	2	0	1	0	25	1	0	1	12	13
+TERT	0	7	0	0	1	0	0	4	0	0	0	1	0	0	0	0	13	0	0	0	12	12
+MET	2	0	0	0	3	0	0	2	3	1	0	1	1	0	0	0	13	2	0	2	11	12
+PPM1D	1	0	2	2	0	0	0	1	0	5	0	1	0	0	0	0	12	1	0	1	11	12
+PTPN11	2	4	0	0	0	0	0	10	0	0	1	0	1	0	0	0	18	0	0	0	10	10
+PTEN	1	0	1	1	1	1	0	4	0	0	2	5	0	0	0	0	16	0	1	1	10	10
+NTRK3	5	2	0	0	3	0	0	2	0	0	0	9	0	0	0	0	21	0	0	0	9	9
+BCOR	0	2	3	0	0	0	0	2	0	2	1	1	1	0	0	0	12	0	0	0	9	9
+BRAF	4	0	0	0	1	0	0	7	0	0	0	4	0	0	0	0	16	0	0	0	8	8
+PIK3R1	2	2	0	0	0	1	1	3	0	1	1	3	0	0	0	0	14	0	0	0	8	8
+ACVR1	3	0	0	0	0	0	0	5	0	0	0	0	1	0	1	0	10	0	0	0	8	8
+ROS1	3	0	0	0	2	0	0	3	0	0	0	1	1	0	0	0	10	0	0	0	8	8
+PDGFRA	0	0	0	0	1	0	0	6	0	0	1	0	1	0	0	0	9	2	0	2	8	10
+KIT	0	0	0	0	2	0	0	3	0	0	0	6	1	1	1	0	14	2	0	2	7	9
+CDK6	1	1	0	0	1	0	0	1	1	0	0	4	1	0	0	0	10	0	0	0	7	7
+IDH1	1	3	0	0	0	0	0	4	0	0	0	0	1	0	1	0	10	0	0	0	7	7
+IGF1R	1	3	0	0	1	0	0	2	0	0	0	13	3	0	0	0	23	1	0	1	6	7
+ATM	0	1	2	0	0	0	0	9	0	1	0	4	2	0	0	0	19	0	0	0	6	6
+KMT2C	1	1	0	0	1	0	0	10	1	0	0	1	3	0	0	0	18	0	0	0	6	6
+TSC2	0	0	1	0	0	0	0	8	0	0	0	0	3	1	0	0	13	0	0	0	6	6
+ALK	0	1	0	0	0	0	0	2	1	2	0	0	2	0	0	0	8	0	0	0	6	6
+NTRK1	0	2	0	0	1	0	0	2	0	0	0	0	1	2	0	0	8	0	0	0	6	6
+SETD2	2	0	1	1	0	0	0	7	0	2	1	1	2	1	0	0	18	0	0	0	5	5
+AKT1	3	0	0	0	0	0	0	0	0	0	0	2	0	1	5	0	11	0	0	0	5	5
+PIK3C2G	2	5	1	0	0	0	0	0	0	0	1	0	1	0	0	0	10	0	0	0	5	5
+TDRD9	1	3	0	0	0	0	0	5	0	0	0	0	1	0	0	0	10	0	0	0	5	5
+CCND1	4	0	0	0	0	0	0	0	1	0	0	4	0	0	0	0	9	1	0	1	5	6
+CCND2	2	1	0	0	0	0	0	0	1	0	0	4	1	0	0	0	9	0	0	0	5	5
+CDKN2A	4	0	1	0	1	0	0	0	0	1	0	1	1	0	0	0	9	0	2	2	5	7
+FGFR1	0	2	0	0	0	0	0	5	0	0	0	1	1	0	0	0	9	0	0	0	5	5
+FYN	1	1	0	0	1	0	0	3	0	0	0	3	0	0	0	0	9	0	0	0	5	5
+FOSB	2	3	0	0	0	0	0	1	0	0	0	1	1	0	0	0	8	0	0	0	5	5
+DDR2	0	1	0	0	2	0	0	1	0	0	0	2	0	0	1	0	7	0	0	0	5	5
+NTRK2	0	0	0	0	2	0	0	1	0	0	0	4	0	0	0	0	7	0	0	0	5	5
+KRAS	4	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	6	0	0	0	5	5
+MYCN	3	7	0	0	0	0	0	5	0	0	0	2	0	0	0	0	17	1	0	1	4	5
+KDM6B	1	1	0	0	0	0	0	5	0	0	0	4	2	0	0	0	13	0	0	0	4	4
+TOP3A	5	2	0	0	0	0	0	3	0	1	0	1	1	0	0	0	13	1	0	1	4	5
+NFIB	5	3	0	0	0	0	0	1	0	0	0	2	1	0	0	0	12	0	0	0	4	4
+CIC	0	1	0	0	1	0	0	6	0	0	1	0	1	0	0	0	10	0	0	0	4	4
+GOLPH3	1	4	0	0	0	0	0	4	0	0	0	1	0	0	0	0	10	0	0	0	4	4
+KDR	0	0	0	0	0	0	0	5	0	0	0	3	2	0	0	0	10	1	0	1	4	5
+MDM2	0	1	0	0	0	0	0	1	0	0	0	6	1	1	0	0	10	0	0	0	4	4
+PIK3C2B	0	1	0	0	0	0	0	5	0	0	0	4	0	0	0	0	10	0	0	0	4	4
+ASXL1	1	1	0	0	0	0	0	5	0	0	0	2	0	0	0	0	9	0	0	0	4	4
+SMARCE1	0	2	0	0	0	0	0	0	0	0	0	5	0	1	1	0	9	0	0	0	4	4
+MAFK	0	1	0	0	0	0	0	0	0	0	0	6	1	0	0	0	8	0	0	0	4	4
+MYC	4	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	8	2	0	2	4	6
+PLAGL2	6	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	8	0	0	0	4	4
+VEGFA	6	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	8	0	0	0	4	4
+PDGFC	0	2	1	0	2	0	0	0	0	0	0	2	0	0	0	0	7	0	0	0	4	4
+CDKN1B	2	2	0	0	0	0	0	0	0	1	0	0	0	0	1	0	6	0	0	0	4	4
+AURKB	1	1	0	0	0	0	0	2	0	0	0	0	1	0	0	0	5	0	0	0	4	4
+GAB2	1	1	0	0	1	0	0	1	0	0	0	0	0	1	0	0	5	0	0	0	4	4
+HIST1H3C	1	3	0	0	0	0	0	1	0	0	0	0	0	0	0	0	5	0	0	0	4	4
+POLE	3	0	0	0	0	0	0	7	0	0	0	0	4	0	0	0	14	0	0	0	3	3
+MTOR	0	0	0	0	0	0	0	5	0	0	0	0	3	0	0	0	8	0	0	0	3	3
+PDGFA	2	3	0	0	0	0	0	2	0	0	0	0	0	1	0	0	8	0	0	0	3	3
+AKT2	1	0	0	0	0	0	0	0	0	0	0	4	2	0	0	0	7	0	0	0	3	3
+NRAS	1	0	0	0	0	0	0	1	0	0	0	5	0	0	0	0	7	0	0	0	3	3
+SLCO1B3	0	3	0	1	0	0	0	3	0	0	0	0	0	0	0	0	7	0	0	0	3	3
+FANCA	0	1	0	0	0	0	0	2	0	0	0	1	1	1	0	0	6	0	0	0	3	3
+YES1	1	2	0	0	0	0	0	0	0	0	0	2	0	0	1	0	6	0	0	0	3	3
+CDKN2C	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	0	4	0	0	0	3	3
+DIS3L2P1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	3	0	0	0	3	3
+HIST1H2BE	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	3	0	0	0	3	3
+CDKN2B	1	6	0	0	0	0	0	1	0	0	0	4	0	0	0	0	12	0	2	2	2	4
+FGFR2	0	0	0	0	0	0	0	3	0	0	1	0	1	0	2	0	7	0	0	0	2	2
+ID3	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	3	0	0	0	2	2
+RB1	0	0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	3	0	0	0	2	2
+TOP2A	0	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	3	0	0	0	2	2
+APOBEC3H	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+HIST1H3B	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+ID2	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+CDK4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	2	1	3
+CDKN1C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+DDX11	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+HIST2H3C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
diff --git a/analyses/oncoprint-landscape/tables/primary-plus_lgat_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary-plus_lgat_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..c0acf24f55
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary-plus_lgat_oncoprint_summary_n.tsv
@@ -0,0 +1,23 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Del	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	Silent	total	MutatedSamples	AlteredSamples
+BRAF	4	0	1	1	109	0	6	39	3	0	0	3	1	167	157	157
+KIAA1549	0	0	0	0	108	0	0	0	0	0	0	0	0	108	108	108
+FGFR1	0	0	0	0	0	0	0	11	0	0	0	0	0	11	7	7
+NTRK2	0	1	0	0	5	0	0	0	0	0	0	0	0	6	6	6
+PIK3CA	0	0	0	0	0	0	0	6	0	0	0	0	0	6	6	6
+QKI	0	0	0	0	1	0	0	0	2	0	0	2	0	5	5	5
+KRAS	0	0	0	0	0	0	0	4	0	0	0	0	3	7	4	4
+RAF1	0	0	0	0	3	0	0	0	1	0	0	0	0	4	4	4
+TP53	0	0	1	0	0	0	0	1	0	0	2	0	0	4	4	4
+CDKN2A	0	2	0	0	0	0	0	0	0	1	0	0	0	3	3	3
+MYB	0	0	0	0	2	0	0	0	1	0	0	0	0	3	3	3
+ROS1	0	0	0	0	3	0	0	0	0	0	0	0	0	3	3	3
+ALK	0	0	0	0	1	0	0	0	1	0	0	0	0	2	2	2
+ATRX	0	0	0	1	0	0	0	0	0	1	0	0	0	2	2	2
+FGFR2	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	2
+NTRK3	2	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2
+H3F3A	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+MAP2K1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
+PRKCA	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1
+PTPN11	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1
+TACC1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1
+TSC1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1
diff --git a/analyses/oncoprint-landscape/data/primary-plus_n_per_cancer_group.tsv b/analyses/oncoprint-landscape/tables/primary-plus_n_per_cancer_group.tsv
similarity index 100%
rename from analyses/oncoprint-landscape/data/primary-plus_n_per_cancer_group.tsv
rename to analyses/oncoprint-landscape/tables/primary-plus_n_per_cancer_group.tsv
diff --git a/analyses/oncoprint-landscape/tables/primary-plus_other_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary-plus_other_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..8fa9cdd08d
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary-plus_other_oncoprint_summary_n.tsv
@@ -0,0 +1,44 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Del	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	5'UTR	Silent	Splice_Region	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+CTNNB1	0	1	0	0	0	0	26	0	0	0	0	0	0	0	27	0	0	0	27	27
+C11orf95	0	1	0	0	17	0	0	3	0	0	0	0	0	0	21	0	0	0	21	21
+RELA	0	0	0	0	17	0	0	2	0	0	0	0	0	0	19	0	0	0	19	19
+NF2	0	0	7	1	2	0	1	1	5	2	0	0	0	0	19	0	0	0	17	17
+BRAF	2	1	0	0	4	0	2	1	0	0	0	0	1	0	11	0	0	0	10	10
+FGFR1	0	0	0	0	3	0	6	0	0	0	0	0	0	0	9	0	0	0	7	7
+TP53	2	0	0	0	1	0	1	0	1	3	0	0	0	1	9	0	0	0	7	7
+TACC1	1	1	0	0	3	0	0	0	0	0	1	2	0	0	8	0	0	0	7	7
+EWSR1	0	1	0	0	6	0	0	0	0	0	0	0	0	0	7	0	0	0	7	7
+KRAS	0	0	0	0	1	0	6	0	0	0	0	0	0	0	7	0	0	0	7	7
+ERBB4	0	0	0	0	4	0	1	0	0	0	0	0	0	0	5	0	0	0	5	5
+TERT	0	1	0	0	1	0	1	0	0	0	0	0	1	0	4	0	0	0	4	4
+MYB	1	0	0	0	1	0	1	0	0	0	0	0	1	0	4	0	0	0	3	3
+MAML2	0	1	0	0	1	0	0	1	0	0	0	0	0	0	3	0	0	0	3	3
+MAMLD1	1	1	0	0	0	0	0	0	0	0	0	0	1	0	3	0	0	0	3	3
+QKI	0	0	0	0	1	0	0	0	0	2	0	0	0	0	3	0	0	0	3	3
+YAP1	0	0	0	0	3	0	0	0	0	0	0	0	0	0	3	0	0	0	3	3
+PDGFRA	0	0	0	0	0	0	2	0	2	0	0	0	0	0	4	0	0	0	2	2
+ARHGAP26	0	1	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+ARL4D	1	1	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+CLDN1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+EGFR	1	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+IDH2	0	1	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	2	2
+L1CAM	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	2	2
+PBRM1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+SETD2	0	0	0	1	0	0	0	0	0	0	1	0	0	0	2	0	0	0	2	2
+AKT1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+AKT3	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+ARID1A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	1	2
+CDC27	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CDKN2A	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+FAM118B	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+FGFR3	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+IDH1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+NTRK2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+PATZ1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	1
+PIK3CA	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+PTEN	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	1
+SMAD4	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	1
+SUFU	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+USP9X	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	1
+MYBL1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
+SMARCB1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
diff --git a/analyses/oncoprint-landscape/tables/primary_only_embryonal_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary_only_embryonal_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..04b9bda1c3
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary_only_embryonal_oncoprint_summary_n.tsv
@@ -0,0 +1,45 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	Splice_Region	Silent	RNA	5'UTR	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+CTNNB1	0	0	0	0	1	0	11	0	0	0	0	0	0	0	0	12	0	0	0	12	12
+DDX3X	0	0	0	0	0	1	7	0	1	1	1	0	0	0	1	12	0	0	0	11	11
+KDM6A	1	0	0	1	0	0	0	0	2	3	1	1	0	0	0	9	0	0	0	9	9
+KMT2C	0	0	2	2	0	0	2	0	1	0	2	0	0	0	0	9	0	0	0	8	8
+KMT2D	0	0	2	2	0	0	1	0	3	1	0	0	0	0	0	9	0	0	0	8	8
+TP53	0	0	0	0	0	0	5	0	1	0	1	0	0	0	0	7	0	0	0	7	7
+SMARCA4	0	1	0	0	0	0	7	0	0	0	0	0	0	0	0	8	0	0	0	6	6
+PTCH1	0	1	3	1	0	0	0	0	0	1	1	0	0	0	0	7	0	0	0	6	6
+KSR2	0	1	0	0	0	0	0	0	0	0	3	0	0	0	0	4	0	0	0	4	4
+TERT	0	3	0	0	0	0	0	0	0	0	0	1	0	0	0	4	1	0	1	3	4
+ATM	0	0	0	0	0	0	2	0	0	0	0	1	0	0	0	3	0	0	0	3	3
+CDK6	0	1	0	0	0	0	0	0	0	0	2	0	0	0	0	3	0	0	0	3	3
+TCF4	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	3	0	0	0	3	3
+ZIC1	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	3	0	0	0	3	3
+APC	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	2	0	0	0	2	2
+CTDNEP1	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	2	0	0	0	2	2
+FOXO3	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	0	0	0	2	2
+GSE1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+IGFN1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	2	0	0	0	2	2
+KBTBD4	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+MIR17HG	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	0	0	2	2
+PRKAR1A	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	2	1	0	1	2	3
+TTYH1	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	2	2	0	2	2	2
+ZMYM3	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	2	0	0	0	2	2
+PTEN	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	2	0	0	0	1	1
+ARID1A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+BCOR	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CENPE	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CREBBP	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1
+DICER1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+DYNC2H1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+MIR512-2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	2	1	3
+MYCN	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	2	0	2	1	3
+OTX2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+PIK3CA	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+SNCAIP	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+SUFU	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	1	1	2
+TBR1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+IDH1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
+MIR1323	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2
+MIR515-2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2
+MIR519C	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	2	0	2
+SMARCB1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	2
+TFPT	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
diff --git a/analyses/oncoprint-landscape/tables/primary_only_hgat_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary_only_hgat_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..52793f84d3
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary_only_hgat_oncoprint_summary_n.tsv
@@ -0,0 +1,82 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Del	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	5'UTR	Splice_Region	3'UTR	Silent	RNA	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+TP53	6	0	0	0	0	0	0	35	0	6	2	0	1	0	2	0	52	0	0	0	35	35
+H3F3A	0	0	0	0	0	0	0	32	0	0	0	0	0	0	0	0	32	0	0	0	32	32
+ATRX	0	1	6	1	2	0	0	7	0	3	1	0	0	1	1	0	23	0	2	2	17	18
+PIK3CA	0	1	0	0	0	4	0	8	0	0	0	0	0	3	0	0	16	0	0	0	12	12
+NF1	1	0	6	1	1	0	0	3	0	6	1	0	0	2	0	0	21	0	0	0	11	11
+EGFR	1	0	0	0	1	0	1	10	0	0	0	1	0	2	1	0	17	1	0	1	10	11
+MET	2	0	0	0	2	0	0	2	3	1	0	0	0	1	1	0	12	2	0	2	10	11
+TERT	0	5	0	0	0	0	0	4	0	0	0	0	0	1	0	0	10	0	0	0	9	9
+PTPN11	1	4	0	0	0	0	0	9	0	0	1	0	0	0	0	0	15	0	0	0	8	8
+PTEN	1	0	1	0	1	0	0	2	0	0	2	0	0	5	0	0	12	0	1	1	7	7
+ACVR1	1	0	0	0	0	0	0	6	0	0	0	0	0	0	1	0	8	0	0	0	7	7
+PPM1D	1	0	1	2	0	0	0	1	0	3	0	0	0	0	0	0	8	0	0	0	7	7
+BCOR	0	1	2	0	0	0	0	2	0	2	1	0	0	0	0	0	8	0	0	0	6	6
+PIK3R1	1	1	0	0	0	1	1	3	0	0	1	0	0	0	0	0	8	0	0	0	6	6
+ROS1	3	0	0	0	1	0	0	3	0	0	0	0	0	1	0	0	8	0	0	0	6	6
+IGF1R	1	3	0	0	1	0	0	0	0	0	0	0	0	9	3	0	17	1	0	1	5	6
+ATM	0	1	2	0	0	0	0	8	0	0	0	0	0	2	1	0	14	0	0	0	5	5
+NTRK3	3	1	0	0	1	0	0	1	0	0	0	0	0	7	0	0	13	0	0	0	5	5
+IDH1	1	2	0	0	0	0	0	3	0	0	0	1	0	0	1	0	8	0	0	0	5	5
+CDK6	0	1	0	0	1	0	0	1	1	0	0	0	0	2	0	0	6	0	0	0	5	5
+PDGFRA	0	0	0	0	1	0	0	4	0	0	0	0	0	0	1	0	6	2	0	2	5	7
+TSC2	0	0	1	0	0	0	0	3	0	0	0	0	0	0	2	0	6	0	0	0	5	5
+SETD2	3	0	1	0	0	0	0	3	0	2	0	0	0	1	1	0	11	0	0	0	4	4
+BRAF	1	0	0	0	1	0	0	4	0	0	0	0	0	4	0	0	10	0	0	0	4	4
+KMT2C	0	1	0	0	1	0	0	6	0	0	0	0	0	0	2	0	10	0	0	0	4	4
+KIT	0	0	0	0	2	0	0	3	0	0	0	0	0	3	1	0	9	2	0	2	4	6
+AKT1	2	0	0	0	0	0	0	0	0	0	0	3	1	1	0	0	7	0	0	0	4	4
+CDKN2A	2	0	1	0	1	0	0	0	0	1	0	0	0	1	0	0	6	0	1	1	4	5
+FYN	1	1	0	0	1	0	0	1	0	0	0	0	0	2	0	0	6	0	0	0	4	4
+ALK	0	1	0	0	0	0	0	1	1	1	0	0	0	0	1	0	5	0	0	0	4	4
+TOP3A	5	2	0	0	0	0	0	3	0	1	0	0	0	1	0	0	12	1	0	1	3	4
+MYCN	2	5	0	0	0	0	0	2	0	0	0	0	0	1	0	0	10	1	0	1	3	4
+KDM6B	0	1	0	0	0	0	0	3	0	0	0	0	0	3	2	0	9	0	0	0	3	3
+CIC	0	1	0	0	1	0	0	5	0	0	1	0	0	0	0	0	8	0	0	0	3	3
+PIK3C2G	1	4	1	0	0	0	0	0	0	0	1	0	0	0	1	0	8	0	0	0	3	3
+SMARCE1	0	2	0	0	0	0	0	0	0	0	0	1	1	4	0	0	8	0	0	0	3	3
+GOLPH3	1	3	0	0	0	0	0	2	0	0	0	0	0	1	0	0	7	0	0	0	3	3
+PIK3C2B	0	1	0	0	0	0	0	3	0	0	0	0	0	3	0	0	7	0	0	0	3	3
+ASXL1	1	1	0	0	0	0	0	2	0	0	0	0	0	2	0	0	6	0	0	0	3	3
+CCND1	4	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	6	0	0	0	3	3
+FGFR1	0	2	0	0	0	0	0	3	0	0	0	0	0	0	1	0	6	0	0	0	3	3
+MDM2	0	0	0	0	0	0	0	1	0	0	0	0	0	5	0	0	6	0	0	0	3	3
+PLAGL2	4	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	6	0	0	0	3	3
+CDKN1B	2	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	5	0	0	0	3	3
+DDR2	0	1	0	0	1	0	0	1	0	0	0	1	0	1	0	0	5	0	0	0	3	3
+FOSB	2	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	5	0	0	0	3	3
+MYC	3	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	5	1	0	1	3	4
+NTRK1	0	0	0	0	1	0	0	2	0	0	0	0	2	0	0	0	5	0	0	0	3	3
+CDKN2C	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	4	0	0	0	3	3
+KRAS	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	3	3
+NTRK2	0	0	0	0	1	0	0	0	0	0	0	0	0	3	0	0	4	0	0	0	3	3
+NFIB	4	2	0	0	0	0	0	1	0	0	0	0	0	0	1	0	8	0	0	0	2	2
+TDRD9	0	2	0	0	0	0	0	4	0	0	0	0	0	0	1	0	7	0	0	0	2	2
+NRAS	1	0	0	0	0	0	0	1	0	0	0	0	0	4	0	0	6	0	0	0	2	2
+POLE	1	0	0	0	0	0	0	4	0	0	0	0	0	0	1	0	6	0	0	0	2	2
+AKT2	1	0	0	0	0	0	0	0	0	0	0	0	0	3	1	0	5	0	0	0	2	2
+CCND2	1	0	0	0	0	0	0	0	0	0	0	0	0	3	1	0	5	0	0	0	2	2
+KDR	0	0	0	0	0	0	0	1	0	0	0	0	0	2	2	0	5	1	0	1	2	3
+PDGFC	0	1	0	0	2	0	0	0	0	0	0	0	0	2	0	0	5	0	0	0	2	2
+MAFK	0	0	0	0	0	0	0	0	0	0	0	0	0	3	1	0	4	0	0	0	2	2
+PDGFA	0	2	0	0	0	0	0	2	0	0	0	0	0	0	0	0	4	0	0	0	2	2
+VEGFA	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	0	0	2	2
+FANCA	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	0	3	0	0	0	2	2
+GAB2	1	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	3	0	0	0	2	2
+HIST1H3C	0	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	3	0	0	0	2	2
+MTOR	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	0	3	0	0	0	2	2
+TOP2A	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	0	3	0	0	0	2	2
+AURKB	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+DIS3L2P1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	0	0	0	2	2
+HIST1H2BE	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	2	0	0	0	2	2
+HIST1H3B	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+SLCO1B3	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+YES1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	2	2
+CDKN2B	1	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	0	1	1	1	2
+FGFR2	0	0	0	0	0	0	0	1	0	0	1	1	0	0	0	0	3	0	0	0	1	1
+APOBEC3H	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CDK4	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	1	2
+HIST2H3C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+ID2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+ID3	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1
+RB1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
diff --git a/analyses/oncoprint-landscape/tables/primary_only_lgat_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary_only_lgat_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..b491babab8
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary_only_lgat_oncoprint_summary_n.tsv
@@ -0,0 +1,23 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	In_Frame_Del	In_Frame_Ins	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	Silent	total	MutatedSamples	AlteredSamples
+BRAF	3	0	1	1	99	0	4	36	2	0	0	2	1	149	140	140
+KIAA1549	0	0	0	0	98	0	0	0	0	0	0	0	0	98	98	98
+FGFR1	0	0	0	0	0	0	0	8	0	0	0	0	0	8	5	5
+NTRK2	0	1	0	0	4	0	0	0	0	0	0	0	0	5	5	5
+PIK3CA	0	0	0	0	0	0	0	5	0	0	0	0	0	5	5	5
+QKI	0	0	0	0	1	0	0	0	2	0	0	2	0	5	5	5
+KRAS	0	0	0	0	0	0	0	4	0	0	0	0	3	7	4	4
+RAF1	0	0	0	0	3	0	0	0	1	0	0	0	0	4	4	4
+MYB	0	0	0	0	2	0	0	0	1	0	0	0	0	3	3	3
+ROS1	0	0	0	0	3	0	0	0	0	0	0	0	0	3	3	3
+TP53	0	0	1	0	0	0	0	1	0	0	1	0	0	3	3	3
+ATRX	0	0	0	1	0	0	0	0	0	1	0	0	0	2	2	2
+FGFR2	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	2
+ALK	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1
+CDKN2A	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+H3F3A	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+MAP2K1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
+NTRK3	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+PRKCA	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1
+PTPN11	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1
+TACC1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	1
+TSC1	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	1
diff --git a/analyses/oncoprint-landscape/data/primary_only_n_per_cancer_group.tsv b/analyses/oncoprint-landscape/tables/primary_only_n_per_cancer_group.tsv
similarity index 100%
rename from analyses/oncoprint-landscape/data/primary_only_n_per_cancer_group.tsv
rename to analyses/oncoprint-landscape/tables/primary_only_n_per_cancer_group.tsv
diff --git a/analyses/oncoprint-landscape/tables/primary_only_other_oncoprint_summary_n.tsv b/analyses/oncoprint-landscape/tables/primary_only_other_oncoprint_summary_n.tsv
new file mode 100644
index 0000000000..f5464618c1
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/primary_only_other_oncoprint_summary_n.tsv
@@ -0,0 +1,40 @@
+Hugo_Symbol	3'Flank	5'Flank	Frame_Shift_Del	Frame_Shift_Ins	Fusion	Missense_Mutation	Multi_Hit_Fusion	Nonsense_Mutation	Splice_Site	3'UTR	5'UTR	Silent	total	Amp	Del	CNV_total	MutatedSamples	AlteredSamples
+CTNNB1	0	1	0	0	0	22	0	0	0	0	0	0	23	0	0	0	23	23
+C11orf95	0	1	0	0	14	0	1	0	0	0	0	0	16	0	0	0	16	16
+RELA	0	0	0	0	14	0	1	0	0	0	0	0	15	0	0	0	15	15
+NF2	0	0	6	1	2	1	0	4	2	0	0	0	16	0	0	0	14	14
+BRAF	1	0	0	0	3	2	1	0	0	0	0	0	7	0	0	0	7	7
+FGFR1	0	0	0	0	3	5	0	0	0	0	0	0	8	0	0	0	6	6
+TACC1	1	1	0	0	3	0	0	0	0	1	1	0	7	0	0	0	6	6
+EWSR1	0	1	0	0	5	0	0	0	0	0	0	0	6	0	0	0	6	6
+KRAS	0	1	0	0	1	3	0	0	0	0	0	0	5	0	0	0	5	5
+ERBB4	0	0	0	0	4	0	0	0	0	0	0	0	4	0	0	0	4	4
+TP53	1	0	0	0	1	0	0	0	3	0	0	0	5	0	0	0	3	3
+QKI	0	0	0	0	1	0	0	0	2	0	0	0	3	0	0	0	3	3
+SETD2	0	0	0	1	1	0	0	0	0	1	0	0	3	0	0	0	3	3
+YAP1	0	0	0	0	3	0	0	0	0	0	0	0	3	0	0	0	3	3
+PDGFRA	0	0	0	0	0	2	0	2	0	0	0	0	4	0	0	0	2	2
+IDH2	0	1	0	0	0	1	0	0	0	0	0	0	2	0	0	0	2	2
+MAML2	0	0	0	0	1	0	1	0	0	0	0	0	2	0	0	0	2	2
+MYB	1	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	2	2
+TERT	0	1	0	0	0	0	0	0	0	0	0	1	2	0	0	0	2	2
+AKT1	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1
+AKT3	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1
+ARHGAP26	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+ARID1A	0	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	1	2
+ARL4D	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CDC27	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CDKN2A	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+CLDN1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+EGFR	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+FAM118B	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+FGFR3	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+IDH1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1
+L1CAM	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	1
+MAMLD1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	1
+PBRM1	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	1
+PIK3CA	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1
+PTEN	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1
+SMAD4	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	1
+MYBL1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
+SMARCB1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1
diff --git a/analyses/oncoprint-landscape/tables/sample_n_in_oncoprint.tsv b/analyses/oncoprint-landscape/tables/sample_n_in_oncoprint.tsv
new file mode 100644
index 0000000000..c32e8596ca
--- /dev/null
+++ b/analyses/oncoprint-landscape/tables/sample_n_in_oncoprint.tsv
@@ -0,0 +1,9 @@
+broad_histology	n_sample	tumor_type
+Low-grade astrocytic tumor	263	primary-plus
+Embryonal tumor	136	primary-plus
+Diffuse astrocytic and oligodendroglial tumor	85	primary-plus
+Other CNS	247	primary-plus
+Low-grade astrocytic tumor	227	primary_only
+Embryonal tumor	128	primary_only
+Diffuse astrocytic and oligodendroglial tumor	61	primary_only
+Other CNS	195	primary_only