R/ArchR_CellCountsHeatmap.R

In alexthiery/scHelper: R package containing helper functions for single cell analysis

#' ArchR function: Plot heatmap of cell counts
#'
#' This function plots a heatmap of cell counts split across two groups
#'
#' @param ArchR ArchR object
#' @param group1 first column to split cells by
#' @param group2 second column to split cells by
#' @return plot generated by pheatmap
#' @export
ArchRCellCountsHeatmap <- function(ArchR = ArchR, group1 = "scHelper_cell_type", group2 = "clusters") {
  group1_data <- getCellColData(ArchR, select = group1)[,1]
  group2_data <- getCellColData(ArchR, select = group2)[,1]
  cM <- confusionMatrix(paste0(group2_data), paste0(group1_data))
  cM <- cM / Matrix::rowSums(cM)
  
  p <- pheatmap::pheatmap(
    mat = cM,
    color = paletteContinuous("whiteBlue"), 
    border_color = "black"
  )
}