R/ch.moralsGetAndPlotDirOverlap.r

In ccpluncw/ccpl_R_chMorals:

#' A function to get and plot directional overlaps by quantity.
#'
#' This function gets and plots directional overlaps by quantity. It simply combines four other functions: ch.moralsGetDirOverlapForAllProbes(); ch.moralsQuantsToGrps(); ch.moralsGetDirOverlapByGrp(); and ch.stripPlotByGrp().
#' @param data a dataframe containing overlap data for probe combinations.
#' @param probe1Col a string the specifies the column name in "data" that contains the first probe item.
#' @param probe2Col a string the specifies the column name in "data" that contains the second probe item.
#' @param overlapCol a string that specifies the name of the column in "data" that contains the overlap column.
#' @param directionCol a string that specifies the name of the column in "data" that contains the direction column that indications the direction of the overlap.
#' @param grpCol a string the specifies the column name in "data" that contains the grouping variable. DEFAULT = NULL
#' @param filename the filename (pdf) to save the figure.  DEFAULT = NULL (file not saved)
#' @return a dataframe with the probe in one column, it's average directional overlap in another, its N in another, followed by separate columns containing the average directional overlap and N for each group.
#' @keywords morals quantity plot directional overlaps
#' @export
#' @examples ch.moralsGetAndPlotDirOverlap (overlapData, "IA1", "IB1", "overlap","direction")

ch.moralsGetAndPlotDirOverlap <- function (data, probe1Col, probe2Col, overlapCol, directionCol, grpCol = NULL, filename=NULL, ...) {

  data.ovrlp.1 <- ch.moralsGetDirOverlapForAllProbes(data, probe1Col, probe2Col, overlapCol, directionCol)
  overOut <- ch.moralsGetDirOverlapByGrp(data.ovrlp.1, probe1Col, grpCol, "dirOverlap")

  if(!is.null(grpCol)) {
    overOut.names <- names(overOut[,])
    overOut.mDO.names  <- sort(grep('meanDO.', overOut.names, value=TRUE))
    overOut.mDO.lgnd <- gsub("meanDO.", "", overOut.mDO.names)

    ### these are for plotting N for each group.  Will implement later.
    # overOut.nDO.names  <- sort(grep('nDO.', overOut.names, value=TRUE))
    # overOut.nDO.lgnd <- gsub("nDO.", "", overOut.nDO.names)

    ch.stripPlotByGrp(overOut, probe1Col, "meanDO", grpCols = overOut.mDO.names, grpLgndNames=overOut.mDO.lgnd, filename = do.filename, yLab = "Directional\nOverlap", ...)
  } else {
    ch.stripPlotByGrp(overOut, probe1Col, "meanDO", filename = do.filename, yLab = "Directional\nOverlap", ...)
  }

  return(overOut)

}