R/get.sraOrgn.R

In palmid: RdRP Analysis Suite

#' get.sraOrgn
#'
#' Retrieve the "scientific_name" for a set of SRA 'run_id'
#'
#' @param run_ids character, SRA 'run_id'
#' @param con     pq-connection, use SerratusConnect()
#' @param ordinal boolean, return 'run_ids' ordered vector [FALSE]
#' @param as.df   boolean, return run_id, date data.frame [FALSE]
#' @return character, string vector
#' @keywords palmid Serratus taxonomy
#' @examples
#' \donttest{
#'  # Retrive a single "scientific_name" 
#' con <- SerratusConnect()
#' palm.orgn   <- get.sraOrgn('SRR9968562', con)
#'
#' # Retrieve an ordered vector of "scientific_name"
#' data( waxsys.palm.sra)
#' waxsys_runs <- waxsys.palm.sra$run_id
#' 
#' waxsys_orgn <- get.sraOrgn(waxsys_runs, con, ordinal = TRUE)
#' 
#' }
#' 
#' @import RPostgreSQL
#' @import dplyr ggplot2
#' @export
# Retrieve date from input of sra run_ids
get.sraOrgn <- function(run_ids, con, ordinal = FALSE, as.df = FALSE) {
  # Bind Local Variables
  run <- scientific_name <- NULL

  # get contigs containing palm_ids
  sra.orgn <- tbl(con, "srarun") %>%
    filter(run %in% run_ids) %>%
    select(run, scientific_name) %>%
    as.data.frame()
    colnames(sra.orgn) <- c("run_id", "scientific_name")

  # must be unique
  sra.orgn <- sra.orgn[ !duplicated(sra.orgn$run_id), ]

  if (ordinal){
    # Left join on palm_ids to make a unique vector
    ord.orgn <- data.frame( run_id = run_ids )
    ord.orgn <- merge(ord.orgn, sra.orgn, all.x = T)
    ord.orgn <- ord.orgn[ match(run_ids, ord.orgn$run_id), ]

    return(ord.orgn$scientific_name)
  } else if (as.df){
    colnames(sra.orgn) <- c("run_id","scientific_name")
  } else {
    sra.orgn <- data.frame( scientific_name = sra.orgn[,2])
  }

  return(sra.orgn)
}