Get drug prediction values for a disease from TxGNN.org server

get_txgnn.R

library(httr2)
library(dplyr)
library(purrr)
library(tibble)
library(dplyr)

##use this table to find your bert_grouped_disease_id
get_disease_map <- function(url = "http://txgnn.org/txgnn_data_v2/node_name_dict.json"){
  id_map <- jsonlite::read_json(url)
  dis_map <- id_map$disease %>% 
    map_df(~ as_tibble(.x), .id = "id") %>% 
    rename(disease_name = value)
  
  return(dis_map)
}

get_drug_map <- function(url = "http://txgnn.org/txgnn_data_v2/node_name_dict.json"){
  id_map <- jsonlite::read_json(url)
  drug_map <- id_map$drug %>% 
    map_df(~ as_tibble(.x), .id = "id") %>% 
    rename(drug_name = value)
  
  return(drug_map)
}

get_disease_id <- function(disease, disease_map = NULL){
  
  if(is.null(disease_map)){
    disease_map <- get_disease_map()
  }

  disease_id <- disease_map |> 
    filter(stringr::str_detect(disease_name, stringr::coll(disease))) |> 
    pull(id) |>
    unique()
  
  if(length(disease_id) == 0){
    stop("Disease id not found")
  } else if(length(disease_id) > 1){
    stop("Multiple disease ids found")
  } else {
    return(disease_id)
  }
}

get_txgnn_drug_predictions <- function(bert_grouped_disease_id, drug_map){
  url <- glue::glue("http://txgnn.org/api/drug_predictions")
  
  resps <-  request(url) |>
    req_url_query(disease_id = bert_grouped_disease_id) |>
    req_perform() 
  
  if(resps$status_code == 200){
    content <- resp_body_json(resps)
    
    df <- content |> 
      map_dfr(~ as_tibble(.x)) %>% 
      left_join(drug_map)
    
  } else {
    stop("Error in API call")
  }
  
}


dm <- get_drug_map()
dism <- get_disease_map()
#neurofibromatosis 
nfid <- get_disease_id("neurofibromatosis", dism)
nf <- get_txgnn_drug_predictions(nfid, dm)
write_csv(nf, './data/txgnn_nf.csv')

#malignant peripheral nerve sheath tumor
mpnstid <- get_disease_id("malignant peripheral nerve sheath tumor", dism)
mpnst <- get_txgnn_drug_predictions(mpnstid, dm)
write_csv(mpnst, './data/txgnn_mpnst.csv')

#plexiform neurofibroma (disease)
pnfid <- get_disease_id("plexiform neurofibroma (disease)", dism)
pnf <- get_txgnn_drug_predictions(pnfid, dm) %>% 
  filter(score != 0)
write_csv(pnf, './data/txgnn_pnf.csv')