R/percentGenes.R

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

#' Examining the VDJ gene usage across clones
#'
#' This function the proportion V or J genes used by 
#' grouping variables. This function only quantifies
#' single gene loci for indicated \strong{chain}. For 
#' examining VJ pairing, please see \code{\link{percentVJ}}.
#'
#' @examples
#' #Making combined contig data
#' combined <- combineTCR(contig_list, 
#'                         samples = c("P17B", "P17L", "P18B", "P18L", 
#'                                     "P19B","P19L", "P20B", "P20L"))
#' percentGenes(combined, 
#'              chain = "TRB", 
#'              gene = "Vgene")
#' 
#' @param input.data The product of \code{\link{combineTCR}}, 
#' \code{\link{combineBCR}}, or \code{\link{combineExpression}}.
#' @param chain "TRA", "TRB", "TRG", "TRG", "IGH", "IGL".
#' @param gene "V", "D" or "J".
#' @param group.by The variable to use for grouping.
#' @param exportTable Returns the data frame used for forming the graph.
#' @param palette Colors to use in visualization - input any 
#' \link[grDevices]{hcl.pals}.
#' @import ggplot2
#' @importFrom stringr str_split str_sort 
#' @importFrom reshape2 melt
#' @export
#' @concept Summarize_Repertoire
#' @return ggplot of percentage of indicated genes as a heatmap
#' 
percentGenes <- function(input.data,
                         chain = "TRB",
                         gene = "Vgene", 
                         group.by = NULL, 
                         exportTable = FALSE, 
                         palette = "inferno") {
  
  sco <- is_seurat_object(input.data) | is_se_object(input.data)
  input.data <- .data.wrangle(input.data, group.by, "CTgene", chain)
  if(!is.null(group.by) & !sco) {
    input.data <- .groupList(input.data, group.by)
  }
  #Parsing gene input
  if (gene %in% c("Vgene", "V", "v", "v.gene")) {
    gene.loci <- paste0(chain, "V")
  } else if(gene %in% c("Jgene", "j", "J", "j.gene")) {
    gene.loci <- paste0(chain, "J")
  } else if(gene %in% c("Dgene", "d", "D", "D.gene")) {
    if(chain %in% c("TRB", "TRD", "IGH")) {
      gene.loci <- paste0(chain, "D")
    } else {
      stop(paste0("There is not the D locus for ", gene))
    }
  }
  #Getting indicated genes across list
  gene_counts <- lapply(input.data, function(x) {
      tmp <- unlist(str_split(x[,"CTgene"], ";"))
      tmp <- str_split(tmp, "[.]", simplify = TRUE)
      
      tmp <- tmp[grep(gene.loci, tmp)]
  })
  #Need total unique genes
  gene.dictionary <- unique(unlist(gene_counts))
  
  #Summarizing the gene usage across the list
  summary <- lapply(gene_counts, function(x) {
                 percentages <- unlist(prop.table(table(x)))
                 genes.to.add <- gene.dictionary [which(gene.dictionary  %!in% names(percentages))]
                 if(length(genes.to.add) >= 1) {
                   percentages.to.add <- rep(0, length(genes.to.add))
                   names(percentages.to.add) <- genes.to.add
                   percentages <- c(percentages, percentages.to.add)
                 }
                 percentages[match(str_sort(names(percentages), numeric = TRUE), names(percentages))]
  })
  
  summary <- do.call(rbind,summary)
  if (exportTable == TRUE) { 
    return(summary) 
  }
  #Melting matrix and visualizing
  mat_melt <- melt(summary)
  plot <- ggplot(mat_melt, aes(y=Var1, x = Var2, fill=round(value*100,2))) +
    geom_tile(lwd= 0.25, color = "black") +
    scale_fill_gradientn(name = "Percentage", colors = .colorizer(palette,21)) +
    theme_classic() + 
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1), 
          axis.title = element_blank())
  return(plot)
}