forked from AlexsLemonade/OpenPBTA-analysis
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Oncoprint output count tables (AlexsLemonade#1191)
- Loading branch information
Showing
16 changed files
with
681 additions
and
11 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
236 changes: 236 additions & 0 deletions
236
analyses/oncoprint-landscape/03-oncoprint-n-count-table.R
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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")) | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.