R/plotRatioBoxes.R

In avastermark19/doseR_development: Test Package of doseR

#' @title plotRatioBoxes Function to boxplot density of ratios between two treatments (using groupings from an annotation column) within a countData object.
#' @description This function plots the expression of the supplied countData object, representing ratios between a pair of selected treatments as a boxplot for each group in the selected annotation column.
#' @usage plotRatioBoxes(cD, groupings, treatment1, treatment2, mode_mean, LOG2,...)
#' @param cD A countData object.
#' @param groupings	A grouping (annotation column), e.g. groupings="something".
#' @param treatment1	Symbol, treatment 1.
#' @param treatment2	Symbol, treatment 2.
#' @param mode_mean 	Boolean, Calculate RowMeans or RowMedians.
#' @param LOG2	Boolean, Calculate LOG2.
#' @param ...	Passthrough arguments to boxplot (additional arguments affecting the summary produced).
#' @details This function boxplots expression of the supplied countData object using ratios of treatment1/treatment2.
#' @return Returns an invisible data frame containing the values.
#' @author AJ Vaestermark, JR Walters.
#' @references The "doseR" package, 2018 (in press).

plotRatioBoxes <- function (cD, groupings= NULL, treatment1=NULL, treatment2=NULL,  mode_mean=TRUE, LOG2=TRUE, ...) {

  #utils::globalVariables(c("."))
 # require(matrixStats)

  MyGroups<-cD@annotation[[groupings]]

  if(is.null(groupings)) {
    stop ('No groupings, e.g. groupings="something"...')
    return (NULL)
  }

  if(length(cD@RPKM) == 0) {
    stop ('No RPKM data saved in count data object... cancelling...')
    return (NULL)
  }

  if(is.null(treatment1) | is.null(treatment2) ) {
    stop ('Indicate treatments, such as  treatment1="A", treatment2="B"')
    return (NULL)
  }

  RM<- (
    if(mode_mean) rowMeans(cD@RPKM[,cD@replicates==treatment1]) else matrixStats::rowMedians(cD@RPKM[,cD@replicates==treatment1])
  ) / (
    if(mode_mean) rowMeans(cD@RPKM[,cD@replicates==treatment2]) else matrixStats::rowMedians(cD@RPKM[,cD@replicates==treatment2])
  )

  if(LOG2) { RM<-log2(RM) }
  RM[is.infinite(RM)]<-NA

  PLOT <- split(RM, MyGroups)

  boxplot(PLOT, ...)

  invisible( PLOT )

}# plotRatioBoxes