R/get.sraGeo.R

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

#' get.sraGeo
#'
#' Retrieve the geo_coordinates for a set of SRA 'run_id'
#'
#' @param run_ids character, SRA 'run_id'
#' @param biosample_ids character, BioSample 'biosample_id'
#' @param con     pq-connection, use SerratusConnect()
#' @param ordinal boolean, return 'run_ids' ordered vector [F]
#' @return data.frame, lon and lat numeric vectors
#' @keywords palmid Serratus geo
#' @examples
#' \donttest{
#' con <- SerratusConnect()
#' palm.geo   <- get.sraGeo(run_ids = "SRR9968562", con = con)
#' }
#' @import RPostgreSQL
#' @import dplyr ggplot2
#' @export
get.sraGeo <- function(run_ids = NULL, biosample_ids = NULL, con, ordinal = FALSE ) {
  # Bind Local Variables
  biosample_id <- coordinate_x <- coordinate_y <- NULL

  if ( is.null(run_ids) & is.null(biosample_ids)){
    stop("Input either 'run_ids' or 'biosamples', not both")
  } else if ( is.null(biosample_ids) ){
    # If run_ids are provided,
    # first convert to biosample_id
    biosample_ids <- get.sraBio(run_ids, con, ordinal = ordinal)
    biosample_ids <- as.character(biosample_ids)
  }

  # get geo_coordinates for biosample
  # NOTE: WARNINGS ARE SUPPRESSED HERE
  #       This table uses 'jsonb' type
  #       which is not supported by
  #       RPostgreSQL
  ##defWarn <- getOption("warn")
  ##options(warn = -1)

  sra.geo <- tbl(con, "biosample_geo_coordinates") %>%
    dplyr::filter(biosample_id %in% biosample_ids) %>%
    select(biosample_id, coordinate_x, coordinate_y) %>%
    as.data.frame()
    colnames(sra.geo) <- c("biosample_id", "lng", "lat")

  if (ordinal){
    # Left join on biosample_ids to make a unique vector
    ord.geo <- data.frame( biosample_id = biosample_ids )
    ord.geo <- merge(ord.geo, sra.geo, all.x = T, by = "biosample_id")
    ord.geo <- ord.geo[ match(biosample_ids, ord.geo$biosample_id), ]

    return(ord.geo)

  } else {
    return(sra.geo)
  }
}