R/cytoBoxplots.R

In cytofast: cytofast - A quick visualization and analysis tool for CyTOF data

#' Draw boxplots for cfList
#'
#' @description Draw boxplots for all given clusters. Values are based on the `counts` slot in the
#' `cfList`.
#'
#' @param cfList a cfList object. It should contain at least data in the 'counts' slot.
#' @param group one of:
#' * a character referring to a column name in the `samples` slot of the `cfList`.
#' * a factor indicating the grouping (x-axis) for the boxplots.
#' @param stat ignore, will be implemented soon.
#'
#' @return None
#'
#' @keywords boxplot,
#'
#' @import ggplot2
#' @importFrom reshape2 melt
#' @importFrom stats median hclust dist
#' @importFrom methods is
#'
#' @examples
#' # Read Data
#' dirFCS <- system.file("extdata", package="cytofast")
#' cfData <- readCytosploreFCS(dir = dirFCS, colNames = "description")
#'
#' # Add cell counts to cfList and add meta data
#' cfData <- cellCounts(cfData, frequency = TRUE, scale = TRUE)
#' meta <- spitzer[match(row.names(cfData@samples), spitzer$CSPLR_ST),]
#' cfData@samples <- cbind(cfData@samples, meta)
#' 
#' # Remove unnecessary markers
#' cfData@expr <- cfData@expr[,-c(3:10, 13:16, 55:59, 61:63)]
#' 
#' # Draw boxplots
#' cytoBoxplots(cfData, group="group")
#' 
#'
#' @export
cytoBoxplots <- function(cfList, group, stat){

  if(!is(cfList, "cfList")){
    stop("first argument is not of class \"cfList\"")
  }

  if(is.null(cfList@counts)){
    stop("`counts` slot is missing from \"cfList\"")
  }

  if(is(group, "character") && length(group) == 1){
    if(group %in% colnames(cfList@samples)){
      grouping <- factor(cfList@samples[,group])
    } else {
        stop("\"group\" is a character, but is missing from `samples` slot ")
      }
  }
  if(is(group, "factor") && length(group) == nrow(cfList@counts)){
    grouping <- group
  }

  plotData <- reshape2::melt(cbind(grouping, data.frame(cfList@counts, check.names=FALSE)), id.vars=1)
  plotData$variable <- factor(plotData$variable, levels=levels(plotData$variable))

  g1 <- ggplot(plotData, aes_string(x="grouping", y="value", color="grouping"))
  g1 + geom_boxplot() +
       geom_point() +
       facet_wrap(. ~ variable, scales = "free") +
       theme_bw() +
       theme(text = element_text(size = 8), axis.text.x = element_blank())
}