R/generate_clustergram.R

In brandonsie/phipcc: Generate Case-Control Reports from PhIP-seq Data

#' generates clustergram of hits
#'
#' @param clustergram_rawdata Output from prepare_clustergram_data or prepare_epitope_clustergram_data
#' @param data_annotated_rbind Annotated hit list from which to generate custom hovertext.
#' @param epitopeSummary Optional epitopefindr group annotation output for custom hovertext.
#' @param ncolors Number of colors to show in clustergram
#'
#' @export


generate_clustergram <- function(clustergram_rawdata, data_annotated_rbind, epitopeSummary = NULL, ncolors = 2){
  my_palette <- colorRampPalette(c("white","black"))(n = ncolors)

  if(!is.null(dev.list())) dev.off()
  png("heatmap.png")
  a <- gplots::heatmap.2(
    clustergram_rawdata,
    key = FALSE, keysize = 0.5, key.title = "RCP>=0.95",
    key.xlab = NA,
    key.ylab = NA,
    #labCol = FALSE, #remove col labels (temp?)
    #labRow = FALSE, #remove row labels (temp?)
    key.xtickfun = function() {
      breaks = pretty(parent.frame()$breaks)
      breaks = breaks[c(1,length(breaks))]
      list(at = parent.frame()$scale01(breaks),labels = breaks)
    },
    col = my_palette,
    margins = c(3, 10),
    trace = "both",
    tracecol = "grey",
    hline = 0,
    vline = 0,
    cexRow = 0.5,
    cexCol = 0.5,
    hclustfun = function(x) hclust(x, method = "ward.D2"),
    distfun = function(x) dist(x, method = "euclidean")^2
  )
  file.remove("heatmap.png")
  if(!is.null(dev.list())) dev.off()

  #store sorted heatmap
  clustergram_sorted <- clustergram_rawdata[rev(a$rowInd), a$colInd]


  # generate custom hovertext
  hovertext <- matrix(nrow = nrow(clustergram_sorted), ncol = ncol(clustergram_sorted))
  for(i in 1:nrow(hovertext)){
    rn <- rownames(clustergram_sorted)[i]
    if(grepl("\\.[0-9]+$", rn)){gsub("\\.[0-9]+$", "", rn)}

    if(!grepl("^Epitope_[0-9]+$", rn)){
      #Normal Annotation
      annot <- data_annotated_rbind$Flags[data_annotated_rbind$ProteinPeptide == rn][1]
      if(is.na(annot)){
        hovertext[i,] <- rn
      } else{

        annot <- paste(annot, collapse = ", ")
        hovertext[i,] <- paste(rn, "|", annot)
      }

    } else if(!is.null(epitopeSummary)){
      #epitopefindr
      group_id <- gsub("Epitope_", "", rn)
      members <- epitopeSummary[,1][epitopeSummary[,group_id] != ""]
      hovertext[i,] <- paste(members, collapse = ", ")
    }

  }

  b <- NULL
  # library(heatmaply)
  # b <- heatmaply(
  #   clustergram_sorted,
  #   main = paste("Candidate Antigen Clustergram"),
  #   colors = my_palette,
  #   fontsize_row = 8,
  #   fontsize_col = 8,
  #   column_text_angle = 90,
  #   margins = c(65, 120),
  #   trace = "both",
  #   tracecol = "grey",
  #   Rowv = FALSE,
  #   Colv = FALSE,
  #   grid_gap = 1,
  #   hide_colorbar = TRUE) %>%
  #   layout(height = 800, width = 900)
  # if(!is.null(dev.list())) dev.off()


  return(list(a, hovertext, clustergram_sorted))
}