R/PlatypusDB_find_CDR3s.R

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

#'CDR3 query function for PlatypusDB
#'
#'@description Queries for the occurrence of CDR3 sequences in public datasets on PlatypusDB.
#' @param VDJ.cdr3s.aa Character A VDJ CDR3s amino acid sequence to search for
#' @param VJ.cdr3s.aa Character A VJ CDR3s amino acid sequence to search for
#' @param projects.to.search Optional character vector. Defaults to "ALL". Names of projects to search within.
#' @return A list of subsets of VDJ matrices from projects
#' containing the query VDJ CDR3 (out[[1]]),
#' the VJ CDR3 (out[[2]]) and cells containing both the query VDJ and VJ CDR3s (out[[3]])
#' @export
#' @examples
#' \dontrun{
#'
#' public_clones <- PlatypusDB_find_CDR3s(VDJ.cdr3s.aa = "CMRYGNYWYFDVW"
#' , VJ.cdr3s.aa = "CLQHGESPFTF", projects.to.search = "ALL")
#'
#' }

PlatypusDB_find_CDR3s <- function(VDJ.cdr3s.aa,
                                  VJ.cdr3s.aa,
                                  projects.to.search){
  platypus_url_lookup <- NULL


  if(missing(VDJ.cdr3s.aa)) VDJ.cdr3s.aa <- c("none")
  if(missing(VJ.cdr3s.aa)) VJ.cdr3s.aa <- c("none")
  if(missing(projects.to.search)) projects.to.search <- "ALL"

  #Get the lookup table
  tryCatch({
  load(url("https://storage.googleapis.com/platypusdb_lookup/platypus_url_lookup.RData"))
    #FOR DEV
    #platypusdb_lookup <- new_lookup

    }, error=function(e){
    message(paste0("Failed to load lookup table. Please verify internet connection \n", e))})

  platypusdb_lookup <- platypus_url_lookup

  if(projects.to.search == "ALL"){
    to_download <- unique(paste0(platypusdb_lookup$project_id, "__CDR3s"))
  } else {
    to_download <- unique(paste0(platypusdb_lookup$project_id[which(platypusdb_lookup$project_id %in% projects.to.search)], "__CDR3s"))
  }

  out.list <- list()
  for(i in 1:length(to_download)){
    url_ <- paste0("https://storage.googleapis.com/platypusdb_cdr3s/", to_download[i], ".RData")

      er <- try(load(url(url_), envir = .GlobalEnv))

      if(inherits(er, "try-error")){
      out.list[[i]] <- get(to_download[i])
      out.list[[i]]$project_id <- stringr::str_split(to_download[i], "__", simplify = T)[,1]
      rm(list = ls(pattern = to_download[i], envir = .GlobalEnv), envir = .GlobalEnv)
      closeAllConnections()
      } else {
      message(paste0("Failed to load ",  to_download[i], ". Skipping this dataset \n"))
      rm(list = ls(pattern = to_download[i], envir = .GlobalEnv), envir = .GlobalEnv)
    }
  }

  out.list <- do.call(rbind, out.list)

  res <- list()

  out.list$VDJ_cdr3s_aa[out.list$VDJ_cdr3s_aa == ""] <- "NOCDR3"
  out.list$VJ_cdr3s_aa[out.list$VJ_cdr3s_aa == ""] <- "NOCDR3"

  for(i in 1:length(VDJ.cdr3s.aa)){
  res[[1]] <- subset(out.list, stringr::str_detect(VDJ.cdr3s.aa[i], out.list$VDJ_cdr3s_aa))
  }

  for(i in 1:length(VJ.cdr3s.aa)){
  res[[2]] <- subset(out.list, stringr::str_detect(VJ.cdr3s.aa[i], out.list$VJ_cdr3s_aa))
  }

  if(length(VDJ.cdr3s.aa) == length(VJ.cdr3s.aa)){
    res.clones <- list()
    for(i in 1:length(VDJ.cdr3s.aa)){
      res.clones[[i]] <- subset(out.list, stringr::str_detect(VJ.cdr3s.aa[i], out.list$VJ_cdr3s_aa) & stringr::str_detect(VDJ.cdr3s.aa[i], out.list$VDJ_cdr3s_aa))
      res.clones$query_clone <- i
    }
    res[[3]] <- do.call(rbind, res.clones)
    names(res) <- c("VDJ CDR3 occurences", "VJ CDR3 occurences", "Clone occurences")
  } else {
    message("Not searching for clones (VDJ and VJ CDR3s), because input vectors are of different lengths")
    names(res) <- c("VDJ CDR3 occurences")
  }
  print("Done")
  return(res)
}