R/plot_v_j_combination.R

In jmzeng1314/IRseq: statistics and visualization for immune repertoire sequencing data

#' visualization for V-J combination
#'
#' It will generate a published quality figure according to the V and J usage marix.
#'
#' @param vj_usage_matrix columns and rows correspond to V and J segments respectively
#' @param image_type cirle/bubble/3D_barplot
#' @param file_out the filename of output figue,should end up with pdf or png
#' @return NULL
#' @import circlize
#' @import RColorBrewer
#' @import reshape
#' @export
#' @keywords combination
#' @examples
#' #' plot_v_j_combination(vj_usage_matrix,'circle','v-j-circle.pdf')

plot_v_j_combination <- function(vj_usage_matrix,image_type,file_out){
  require(circlize); require(RColorBrewer)
  require(ggplot2); require(reshape); require(RColorBrewer)
  rn = rownames(vj_usage_matrix)
  cn = colnames(vj_usage_matrix)
  mat <-vj_usage_matrix* 100
  n <- nrow(vj_usage_matrix)
  m <- ncol(vj_usage_matrix)
  # Here columns and rows correspond to V and J segments respectively

  # plotting function for simplicity
  my.bubble.plot <- function(...){
    df.m <- cbind(expand.grid(dimnames(mat)), value = as.vector(mat))
    #head(df.m)
    colnames(df.m)=c("J_type" ,"V_type" ,"Percent" )
    image=ggplot(df.m,aes(x=V_type,y=J_type))+
      geom_point(aes(size=Percent,fill=J_type),shape=21,colour="black")+
      scale_size_area(max_size=15)+scale_fill_hue(guide = "none")+
      theme_set(theme_bw(base_size=20))+
      theme(text=element_text(face='bold'),axis.text.x=element_text(angle=45,hjust=1,size=10),
            axis.title.x=element_blank())+labs(title='Bubble',y="J type")
    print(image)
  }

  my.3d.plot <- function(...){

  }

  my.circle.plot <- function(...) {
    # sort

    col_sum = apply(mat, 2, sum)
    row_sum = apply(mat, 1, sum)

    mat <- mat[order(row_sum), order(col_sum)]

    # equal number of characters for visualizaiton

    rn <- rownames(mat)
    cn <- colnames(mat)

    maxrn <- max(nchar(rn))
    maxcn <- max(nchar(cn))

    for(i in seq_len(length(rn))) {
      rn[i] <- paste(rn[i], paste(rep(" ", maxrn - nchar(rn[i])), collapse = ''))
    }

    for(i in seq_len(length(cn))) {
      cn[i] <- paste(cn[i], paste(rep(" ", maxcn - nchar(cn[i])), collapse = ''))
    }

    rownames(mat) <- rn
    colnames(mat) <- cn

    # viz using circlize
    circos.par(gap.degree = c(rep(1, nrow(mat)-1), 10, rep(1, ncol(mat)-1), 15), start.degree = 5)

    rcols <- rep(brewer.pal(12, "Paired"), nrow(mat)/12 + 1)[1:nrow(mat)]
    ccols <- rep(brewer.pal(12, "Paired"), ncol(mat)/12 + 1)[1:ncol(mat)]

    names(rcols) <- sort(rownames(mat))
    names(ccols) <- sort(colnames(mat))

    chordDiagram(mat, annotationTrack = "grid",
                 grid.col = c(rcols, ccols),
                 preAllocateTracks = list(track.height = 0.2), transparency = 0.5)

    circos.trackPlotRegion(track.index = 1, bg.border = NA,
                           panel.fun = function(x, y) {
                             sector.name = get.cell.meta.data("sector.index")
                             xlim = get.cell.meta.data("xlim")
                             ylim = get.cell.meta.data("ylim")
                             circos.text(mean(xlim), ylim[1], cex = 0.5, sector.name, facing = "clockwise", adj = c(0, 0.5))
                           }
    )

    circos.clear()

  }

  custom.dev <- function(fname) {
    if (grepl("\\.pdf$",fname)){
      pdf(fname)
    } else if (grepl("\\.png$",fname)) {
      png(fname, width     = 3.25,
          height    = 3.25,
          units     = "in",
          res       = 1200,
          pointsize = 4)
    } else {
      stop('Unknown plotting format')
    }
  }

  if(hasArg(file_out)){
    custom.dev(file_out)
    if(image_type=='circle'){
      my.circle.plot()
    }else if (image_type=='bubble'){
      my.bubble.plot()
    }else if(image_type=='3D_barplot'){
      my.3d.plot()
    }else {
      stop('Unknown image type, must be circle or bubble or 3D_barplot !')
    }
    dev.off()
  }else{
    if(image_type=='circle'){
      my.circle.plot()
    }else if (image_type=='bubble'){
      my.bubble.plot()
    }else if(image_type=='3D_barplot'){
      my.3d.plot()
    }else {
      stop('Unknown image type, must be circle or bubble or 3D_barplot !')
    }
  }



}