doseR_0.99.4: doseR

#' @title plotRatioBoxes Function to boxplot density of ratios
#' between two treatments (using groupings from an annotation column)
#' within a countDat object.
#' @description This function plots the expression of the supplied
#' countDat object, representing ratios between a pair of selected
#' treatments as a boxplot for each group in the selected annotation column.
#' @usage plotRatioBoxes(cD, groupings= NULL, treatment1=NULL, treatment2=NULL,
#' mode_mean=TRUE, LOG2=TRUE, ...)
#' @param cD A countDat 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 countDat
#' object using ratios of treatment1/treatment2.
#' @return Returns an invisible data frame containing the values.
#'
#' @examples
#' data(hmel.data.doser)
#' reps <- c("Male", "Male", "Male", "Female", "Female", "Female")
#' annotxn <- data.frame("Chromosome" = factor(hmel.dat$chromosome,
#' levels = 1:21))
#' hm.tr<-hmel.dat$trxLength
#' hm<-new("countDat",data=hmel.dat$readcounts,seglens=hm.tr,
#' annotation=annotxn)
#' replicates(hm) <- reps
#' libsizes(hm) <- getLibsizes2(hm, estimationType = "total")
#' rpkm(hm) <- make_RPKM(hm)

#' plotRatioBoxes(hm, groupings='Chromosome', treatment1 = 'Male',
#' treatment2 = 'Female')
#'
#'
#' @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, ...) {

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