Patch/cbioportal utils

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: nfportalutils
 Title: NF Portal Utilities
-Version: 0.0.0.9320
+Version: 0.0.0.9400
 Authors@R: c(
     person(given = "Robert", family = "Allaway", role = c("aut", "cre"),
            email = "[email protected]",

NAMESPACE

@@ -27,6 +27,10 @@ export(as_table_schema)
 export(assign_study_data_types)
 export(bad_url)
 export(calculate_related_studies)
+export(cbp_add_cna)
+export(cbp_add_expression)
+export(cbp_add_maf)
+export(cbp_new_study)
 export(check_access)
 export(check_readpair_validity)
 export(check_wiki_links)
@@ -43,7 +47,6 @@ export(grant_specific_file_access)
 export(key_label_to_id)
 export(make_admin)
 export(make_folder)
-export(make_meta_study)
 export(make_public)
 export(make_public_viewable)
 export(map_sample_input_ss)
@@ -64,7 +67,6 @@ export(remove_button)
 export(remove_wiki_subpage)
 export(summarize_file_access)
 export(syn_login)
-export(syncBP_maf)
 export(table_query)
 export(update_study_annotations)
 export(use_latest_in_collection)

R/cbioportal.R

@@ -0,0 +1,242 @@
+# Export data from Synapse as a cBioPortal dataset, where different data types can be added to the package one-by-one,
+# much in the spirit of https://github.com/r-lib/usethis.
+# This file contains the higher-level wrappers that are user-facing.
+# See `cboilerplate.R` for the lower-level utils, which allows more control.
+# All functions should start with `cbp_*` so that it's clear this is cBioPortal-relevant functionality.
+
+#' Enumerate combinations of valid cBP data types and data subtypes and helper utils if available
+#' 
+#' https://docs.cbioportal.org/file-formats/
+#' 
+#' @keywords internal
+cbp_datatypes <- function() {
+
+  types <- data.table::rbindlist(list(
+    list("CLINICAL", "SAMPLE_ATTRIBUTES", "cbp_add_clinical", ""),
+    list("CLINICAL", "PATIENT_ATTRIBUTES", "cbp_add_clinical", ""),
+    list("COPY_NUMBER_ALTERATION", "SEG", "cbp_add_cna", "default"),
+    list("COPY_NUMBER_ALTERATION", "DISCRETE", "", ""),
+    list("COPY_NUMBER_ALTERATION", "DISCRETE_LONG", "", ""),
+    list("COPY_NUMBER_ALTERATION", "CONTINUOUS", "", ""),
+    list("COPY_NUMBER_ALTERATION", "LOG2-VALUE", "", ""),
+    list("MRNA_EXPRESSION", "CONTINUOUS", "cbp_add_expression", ""),
+    list("MRNA_EXPRESSION", "Z-SCORE", "cbp_add_expression", ""),
+    list("MUTATION_EXTENDED", "MAF", "cbp_add_maf", ""),
+    list("METHYLATION", "CONTINUOUS", "", ""),
+    list("PROTEIN_LEVEL", "LOG2-VALUE", "", ""),
+    list("STRUCTURAL_VARIANT", "SV", "", "")))
+
+  setnames(types, c("dataType", "dataSubtype", "util", "note"))
+  return(types)
+}
+
+#' Initialize a new cBioPortal study dataset
+#' 
+#' Create a new directory with a basic required [study meta file](https://docs.cbioportal.org/file-formats/#meta-file),
+#' much like how we'd create a new R package and put a DESCRIPTION file in it.
+#' 
+#' @param cancer_study_identifier Cancer study identifier in format such as `nst_nfosi_ntap_2022`.
+#' @param name Name of the study, e.g. "Malignant Peripheral Nerve Sheath Tumor (NF-OSI, 2022)".
+#' @param type_of_cancer Id for type of cancer. If `validate` is TRUE, this is one of the things validated with warning if mismatched.
+#' @param description Description of the study, defaults to a generic description that can be edited later.
+#' @param short_name (Optional) Short name for the study.
+#' @param citation (Optional) A relevant citation, e.g. "TCGA, Nature 2012".
+#' @param pmid (Optional) One or more relevant pubmed ids (comma-separated, no whitespace); if used, citation cannot be `NULL`.
+#' @param groups (Optional) Defaults to "PUBLIC" for use with public cBioPortal; 
+#' otherwise, use group names that makes sense with the configuration of your cBioPortal instance.
+#' @param add_global_case_list (Optional) Use `NULL` to ignore, default is `TRUE` for an "All samples" case list( to be generated automatically.
+#' @param validate Validate against public cBioPortal configuration. Default `TRUE`, 
+#' but might want to set to `FALSE` especially if using a custom cBioPortal instance with different configuration. 
+#' @param verbose Whether to be chatty.
+#' 
+#' @export
+cbp_new_study <- function(cancer_study_identifier,
+                          name,
+                          type_of_cancer,
+                          description = "The data are contributed by researchers funded by the Neurofibromatosis Therapeutic Acceleration Program (NTAP). The reprocessing of the raw data is managed by the NF Open Science Initiative (https://nf.synapse.org/).",
+                          short_name = NULL,
+                          citation = NULL,
+                          pmid = NULL,
+                          groups = "PUBLIC",
+                          add_global_case_list = TRUE,
+                          validate = TRUE,
+                          verbose = TRUE) {
+
+  # TODO Validate study id
+  study_dir <- cancer_study_identifier
+  if(!dir.exists(study_dir)) {
+    if(verbose) checked_message(glue::glue("Creating {study_dir} study directory"))
+    dir.create(glue::glue("./{study_dir}"))
+  }
+
+  checked_message("Setting dataset directory as working directory")
+  setwd(study_dir)
+
+  if(validate) {
+    tryCatch({
+      cancer_ids <- httr::GET("https://www.cbioportal.org/api/cancer-types?direction=ASC&pageNumber=0&pageSize=10000&projection=SUMMARY") %>% 
+        httr::content() %>%
+        sapply(`[[`, "cancerTypeId")
+      if(!type_of_cancer %in% cancer_ids) {
+        warning("Specified `type_of_cancer id` isn't in the public list. 
+                Check for typos or include additional meta for this cancer type -- see https://docs.cbioportal.org/file-formats/#cancer-type")
+      }
+    }, error = function(e) warning("Note: Other issue with validation via public API...skipping."))
+  }
+
+  df_file <- make_meta_study_generic(cancer_study_identifier = cancer_study_identifier,
+                                     type_of_cancer = type_of_cancer, 
+                                     name = name, 
+                                     description = description, 
+                                     citation = citation,
+                                     pmid = pmid,
+                                     groups = groups, 
+                                     short_name = short_name,
+                                     add_global_case_list = add_global_case_list)
+
+  write_meta(df_file, "meta_study.txt", verbose = verbose)
+  if(verbose) checked_message("Study meta added")
+}
+
+# ------------------------------------------------------------------------------- #
+
+
+#' Export and add clinical data to cBioPortal dataset
+#' 
+#' This should be run in an existing dataset package root. 
+#'
+#' Clinical data are mapped and exported according to a reference mapping. 
+#' Also reformatting of `PATIENT_ID`, `SAMPLE_ID` to contain only letters, numbers, points, underscores, hyphens;
+#' in Nextflow processing any spaces gets replaced with underscores so that's the default here.
+#' Does *not* check for missing samples, as final validation via cBioPortal tool is still expected for that.
+#' 
+#' @param ref_view A view that contains all clinical data for the study.
+#' @param ref_map YAML file specifying the mapping of (NF) clinical metadata to cBioPortal model. See details.
+#' @param verbose Whether to provide informative messages throughout.
+cbp_add_clinical <- function(ref_view,
+                             ref_map,
+                             verbose = TRUE) {
+
+  cancer_study_identifier <- check_cbp_study_id()
+
+  if(verbose) checked_message("Pulling the clinical data from Synapse")
+  df <- get_clinical_data_for_cbp_study(ref_view)
+
+  if(verbose) checked_message("Formatting and making clinical data file(s)")
+  df$specimenID <- gsub(" ", "_", clinical_data$specimenID)
+  write_cbio_clinical(df, ref_map = ref_map, verbose = verbose)
+
+  if(verbose) checked_message("Making sample clinical meta file")
+  make_meta_sample(cancer_study_identifier, verbose = verbose)
+
+  # Before making meta, check that the optional patient data file was written 
+  if(file.exists("data_clinical_patient.txt")) {
+    if(verbose) checked_message("Making patient clinical meta file")
+    make_meta_patient(cancer_study_identifier, verbose = verbose)
+  }
+
+  if(verbose) checked_message("Done with adding clinical data")
+
+}
+
+#' Check that in valid cBioPortal study dataset root
+#' 
+#' The `cbp_add*` functions need to be run while in the study package root.  
+#' This checks in valid study directory and returns the `cancer_study_id`.
+#' 
+#' @keywords internal
+#' @return `cancer_study_id` for the current cBioPortal cancer study.
+check_cbp_study_id <- function() {
+
+  tryCatch({
+
+    suppressWarnings({
+      study <- yaml::read_yaml("meta_study.txt")
+      study$cancer_study_identifier
+    })
+
+  }, error = function(e) stop("The path ", getwd(), 
+                              " does not appear to be a valid cBioPortal study.", 
+                              call. = FALSE))
+}
+
+# ------------------------------------------------------------------------------- #
+
+#' Export and add mutations data to cBioPortal dataset
+#' 
+#' This should be run in an existing dataset package root.
+#' 
+#' Get merged maf file that represents filtered subset of `maf`s containing only (non-germline) data OK to release publicly.
+#' This needs to be packaged with other files like this
+#' [example of a public mutations dataset](https://github.com/cBioPortal/datahub/tree/1e03ea6ab5e0ddd497ecf349cbee7d50aeebcd5e/public/msk_ch_2020).
+#' 
+#' @inheritParams cbp_new_study
+#' @param maf_data Synapse id of `merged maf` file for public release.
+#' @export
+cbp_add_maf <- function(maf_data, verbose = TRUE) {
+
+  .check_login()
+  cancer_study_identifier <- check_cbp_study_id()
+
+  if(verbose) checked_message("Getting `maf_data` file from Synapse")
+  file <- .syn$get(maf_data, downloadLocation = ".")
+  data_mutations <- sub(file$name, "data_mutations.txt", file$path)
+  file.rename(file$path, data_mutations)
+
+  if(verbose) checked_message("Making maf meta file")
+  make_meta_maf(cancer_study_identifier, verbose = verbose)
+
+  if(verbose) checked_message("Done with adding MAF data")
+
+}
+
+
+# ------------------------------------------------------------------------------- #
+
+#' Export and add CNA (seg) data to cBioPortal dataset
+#' 
+#' This should be run in an existing dataset package root.
+#' 
+#' @inheritParams cbp_new_study
+#' @param cna_data Synapse id of CNA data file, currently only handles `.seg` file.
+#' @export
+cbp_add_cna <- function(cna_data, verbose = TRUE) {
+
+  cancer_study_identifier <- check_cbp_study_id()
+
+  if(verbose) checked_message("Getting the CNA (.seg) data file from Synapse")
+  file <- .syn$get(cna_data, downloadLocation = ".")
+  data_cna <- sub(file$name, "data_cna.seg", file$path)
+  file.rename(file$path, data_cna)
+
+  if(verbose) checked_message("Making the meta file")
+  make_meta_cna(cancer_study_identifier)
+
+  if(verbose) checked_message("Done with adding CNA data")
+
+} 
+
+
+#' Export and add expression data to cBioPortal dataset
+#' 
+#' This should be run in an existing dataset package root.
+#' 
+#' @inheritParams cbp_new_study
+#' @param expression_data Syn id of gene expression data.
+#' @export
+cbp_add_expression <- function(expression_data, verbose = TRUE) {
+
+  cancer_study_identifier <- check_cbp_study_id()
+
+  if(verbose) checked_message("Getting the mRNA expression data file from Synapse")
+  file <- .syn$get(expression_data, downloadLocation = ".")
+  data_expression <- sub(file$name, "data_expression.txt", file$path)
+  file.rename(file$path, data_expression)
+
+  if(verbose) checked_message("Making the meta file")
+  make_meta_expression(cancer_study_identifier)
+
+  if(verbose) checked_message("Done with adding expression data")
+
+} 
+