R/cell.count.bx.R

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

#' Boxplot according according metadata
#'
#' This function draws a boxplot according to the cell count for a specified condition.
#' @param fcs.SCE A \code{fcs.SCE} object generated through \code{\link[FlowCT:fcs.SCE]{FlowCT::fcs.SCE()}}.
#' @param assay.i Name of matrix stored in the \code{fcs.SCE} object from which calculate correlation. Default = \code{"normalized"}.
#' @param x.axis Variable name (from \code{colData(fcs.SCE)}) for drawing the x-axis in plot.
#' @param color.by Variable name (from \code{colData(fcs.SCE)}) for coloring the plot. Default = \code{x.axis} (i.e., the same specfied in \code{x.axis}).
#' @param label.by Variable from (from \code{colData(fcs.SCE)}) for labeling. Default = \code{NULL}.
#' @param limits Numeric vector with limits for plotting (minimum, maximum). Default = \code{NULL} (i.e., automatically calculated from data).
#' @param colors Vector with colors for plotting. Default = \code{NULL} (i.e., it will choose automatically a vector of colors according to \code{\link[FlowCT:div.colors]{FlowCT::div.colors()}}).
#' @keywords cell count
#' @keywords boxplot
#' @export
#' @import ggplot2
#' @importFrom SingleCellExperiment colData
#' @importFrom SummarizedExperiment assay
#' @examples
#' \dontrun{cell.count.bx(fcsL, assay.i = "normalized", x.axis = "condition")}

cell.count.bx <- function(fcs.SCE, assay.i = "normalized", x.axis, color.by = x.axis, label.by = NULL, limits = NULL, colors = NULL){
  if (!requireNamespace("ggpubr", quietly = TRUE)) stop("Package \"ggpubr\" needed for this function to work. Please install it.", call. = FALSE)

  data <- cbind(colData(fcs.SCE), t(assay(fcs.SCE, i = assay.i)))
  ggdf <- data.frame(data[!duplicated(data[,"filename"]),], cell_counts = as.numeric(table(data[,"filename"])))

  if(is.null(limits)) limits <- c(min(ggdf$cell_counts), max(ggdf$cell_counts))
  if(is.null(colors)) colors <- div.colors(length(unique(ggdf[,color.by])))

  g <- ggpubr::ggboxplot(ggdf, x = x.axis, y = "cell_counts", fill = color.by) +
    ggpubr::stat_compare_means(label.x = 1.7, label.y = max(ggdf$cell_counts)) +
    scale_y_continuous(limits = limits) +
    scale_fill_manual(values = colors) +
    theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.background = element_blank(),
          axis.line = element_line(colour = "black"))+
    geom_jitter(shape = 16, position = position_jitter(0.2))

  if(!is.null(label.by)){
    if (!requireNamespace("ggrepel", quietly = TRUE)) stop("Package \"ggrepel\" needed for this function to work. Please install it.", call. = FALSE)
    g <- g + ggrepel::geom_label_repel(aes(label = eval(parse(text = label.by))), alpha = 0.75, fontface = 'bold', color = 'black')
  }

  return(g)
}