R/count_studies.R

In Dahaniel/DoOR.functions: Integrating Heterogeneous Odorant Response Data into a Common Response Model: A DoOR to the Complete Olfactome

#' count_studies
#'
#' returns a matrix indiating how many studies have recorded individual
#' receptor-odorant combinations
#'
#' @param ors data.frame containing all receptors exidting in DoOR.
#' @param odor_data data.frame containing information about the odorants in
#'   DoOR.
#' @param char.columns number of character columns in each receptor data.frame.
#' @param ident odorant identifier to be used as rownames.
#' @export
#' @aliases countStudies count_studies
#'
#' @return matrix
#'
#' @examples
#' # load some data
#' library(DoOR.data)
#' load_door_data(nointeraction = TRUE)
#'
#' #run count studies and plot the result
#' count <- count_studies()
#' image(count)
#' head(count)
#'
count_studies <- function(ors = door_default_values("ORs"),
                         odor_data = door_default_values("odor"),
                         char.columns = door_default_values("num.charColumns"),
                         ident = door_default_values("ident")) {
  counts <- matrix(nrow = dim(odor_data)[1], dimnames = c(odor_data[ident]))
  for (i in seq_along(ors$OR)) {
    or.name <- as.character(ors$OR[i])
    or <- get(or.name)
    or <- or[-c(1:char.columns)]
    or <- !is.na(or)
    or <- apply(or, 1, sum)
    if(i == 1) {
      counts[,1] <- or
    } else {
      counts <- cbind(counts,  or)
    }
    colnames(counts)[i] <- or.name
  }
  return(counts)
}