pretty_cnv_heatmap.R

#' Plot a CNV heatmap
#' \code{cnv_data} must have the following columns:
#' 
#' - start (start position of each region)
#' - chr (chromosome)
#' - single_cell_id (id of each cell)
#' - clone (clone to which each cell is assigned)
#' - copy_number (copy number of each clone in region)
#' 
#' @export
plot_cnv_heatmap <- function(cnv_data) {
  cnv_cols <- c("0" = "#2166ac",
                "1" = "#92c5de", 
                "2" = "grey80", 
                "3" = "#f4a582", 
                "4" = "#d6604d",
                "5" = "#b2182b",
                "6+" = "#67001f")
  
  chr_levels <- c(as.character(1:23), "X", "Y")
  cnv_data$chr <- factor(cnv_data$chr, levels = chr_levels)
  cnv_data$copy_number[cnv_data$copy_number >= 6] <- "6+"
  
  cnv_data$copy_number <- as.character(cnv_data$copy_number)
  
  
  ggplot(cnv_data, aes(x = start, y = single_cell_id, fill = copy_number)) +
    geom_raster() +
    facet_grid(clone ~ chr, scales = "free", space = "free", switch = "both") +
    scale_fill_manual(values = cnv_cols, name = "Copy Number") +
    labs(x = "Chromosome", y = "Clone") +
    theme(axis.text = element_blank(),
          axis.ticks = element_blank(),
          strip.background = element_rect(fill = 'white'),
          legend.position = "bottom")
}