R/plotAB.R

In JordanVeldboom/compartmap: A/B compartment inference from ATAC-seq and methylation array data

#' Plots A/B compartment estimates on a per chromosome basis
#'
#' Plot A/B compartments bins
#'
#' @param x      The matrix obejct returned from getCompartments
#' @param chr    Chromosome to subset to for plotting
#' @param main    Title for the plot
#' @param ylim      Y-axis limits (default is -1 to 1)
#' @param unitarize   Should the data be unitarized? (not explicitly necessary for arrays)
#' @param reverse    Reverse the sign of the PC values?
#' @param top.col    Top (pos. PC values) chromatin color to be plotted
#' @param bot.col    Bottom (neg. PC values) chromatin color to be plotted
#' @param with.ci    Whether to plot confidence intervals
#' @param filter    Whether to filter eigenvalues close to zero (default: TRUE)
#' @param filter.lower.bound    The minimum absolute eigenvalue to include in the plot
#' @param median.conf    Whether to plot the median confidence estimate across the chromosome
#' 
#' @return    invisibly, the compartment estimates from the plot
#' 
#' @import    GenomicRanges
#' 
#' @export 
#' 
#' @examples 
#' 
#' library(GenomicRanges)
#' library(Homo.sapiens)
#' 
#' #Generate random genomic intervals of 1-1000 bp on chr1-22
#' #Modified from https://www.biostars.org/p/225520/
#' random_genomic_int <- data.frame(chr = rep("chr14", 100))
#' random_genomic_int$start <- apply(random_genomic_int, 1, function(x) { round(runif(1, 0, getSeqLengths(chr = x)[[1]]), 0) })
#' random_genomic_int$end <- random_genomic_int$start + runif(1, 1, 1000)
#' random_genomic_int$strand <- "*"
#' 
#' #Generate random counts
#' counts <- rnbinom(1000, 1.2, 0.4)
#' 
#' #Build random counts for 10 samples
#' count.mat <- matrix(sample(counts, nrow(random_genomic_int) * 10, replace = FALSE), ncol = 10)
#' colnames(count.mat) <- paste0("sample_", seq(1:10))
#' 
#' #Bin counts
#' bin.counts <- getBinMatrix(count.mat, makeGRangesFromDataFrame(random_genomic_int), chr = "chr14", genome = "hg19")
#' 
#' #Calculate correlations
#' bin.cor.counts <- getCorMatrix(bin.counts)
#' 
#' #Get A/B signal
#' absignal <- getABSignal(bin.cor.counts)
#' 
#' #Plot the A/B signal
#' par(mar=c(1,1,1,1))
#' par(mfrow=c(1,1))
#' plotAB(absignal$pc, ylim = c(-0.2, 0.2), unitarize = TRUE)
#' 
#' \dontrun{
#' #If plotting individual A/B signals using output from getCompartments
#' #Note: this function currently only supports plotting individual chromosomes from single samples
#' bin.chr1.ab <- getCompartments(data, "array", chrs = "chr1", genome = "hg19")
#' 
#' #For 7 samples
#' #Adjust ylim as necessary
#' par(mar=c(1,1,1,1))
#' par(mfrow=c(7,1))
#' plotAB(bin.chr1.ab[,1], ylim = c(-0.2, 0.2), unitarize = TRUE)
#' plotAB(bin.chr1.ab[,2], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "goldenrod")
#' plotAB(bin.chr1.ab[,3], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "darkblue")
#' plotAB(bin.chr1.ab[,4], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "red")
#' plotAB(bin.chr1.ab[,5], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "black")
#' plotAB(bin.chr1.ab[,6], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "cyan")
#' plotAB(bin.chr1.ab[,7], ylim = c(-0.2, 0.2), unitarize = TRUE, top.col = "seagreen")
#' }



plotAB <- function(x, chr = NULL, what = c("score", "flip.score"), main="",ylim=c(-1, 1),
                   unitarize=FALSE, reverse=FALSE, top.col = "deeppink4", bot.col = "grey50",
                   with.ci = FALSE, filter = TRUE, filter.min.eigen = 0.02,
                   median.conf = FALSE){
  #what are we plotting
  what <- match.arg(what)
  #check if plotting CI
  if (with.ci) {
    if (is(x, "GRanges")) {
      if (!is.null(chr)) x <- keepSeqlevels(x, chr, pruning.mode = "coarse")
      if (("conf.est" %in% names(mcols(x)))) {
        if (filter) x <- x[abs(as(mcols(x)[what], "matrix")) > filter.min.eigen,]
        x.mat <- as(mcols(x)[what], "matrix")
        if (unitarize) x.mat <- .unitarize(x.mat)
        x.mat <- as.numeric(x.mat)
        if (reverse) x.mat <- -x.mat
        n <- length(x.mat)
        col <- rep(top.col, n)
        col[x.mat<0] <- bot.col
        par(mar=c(1,5,1,1))
        par(mfrow=c(2,1))
        barplot(x.mat, ylim=ylim, 
                bty="n", xlab="", ylab="Eigenvector",border=col, col=col, main=main)
        if (median.conf) {
          barplot(x$conf.est, ylim=c(0,1), ylab="Compartment confidence estimates")
          abline(h = median(x$conf.est), col = "red", lty = 2, lwd = 3)
        } else {
          barplot(x$conf.est, ylim=c(0,1), ylab="Compartment confidence estimates") 
          }

      } else {
        message("conf.est isn't found in the mcols() of the input")
        stop("Run the compartmentCI() first.")
      }
    } else {
      stop("Input needs to be a GRanges object.")
    }
  } else {
    if (is(x, "GRanges")) {
      if (!is.null(chr)) x <- keepSeqlevels(x, chr, pruning.mode = "coarse")
      x <- switch(what,
                  score = as(x$pc, "matrix"),
                  flip.score = as(x$flip.score, "matrix"))
    }
    if (unitarize) x <- .unitarize(x)
    if (filter) x <- x[abs(x) > filter.min.eigen]
    x <- as.numeric(x)
    if (reverse) x <- -x
  
    n <- length(x)
    col <- rep(top.col, n)
    col[x<0] <- bot.col
    barplot(x, ylim=ylim, 
            bty="n", xlab="", ylab="Eigenvector", border=col, col=col, main=main)
    }
  }

.unitarize <- function(x, medianCenter = TRUE) {
  if (medianCenter) x <- x - median(x, na.rm = TRUE)
  bad <- is.na(x)
  x[!bad] <- x[!bad] / sqrt(sum(x[!bad]^2))
  n.bad <- sum(bad)
  if (n.bad > 0) {
    message(
      sprintf("[.unitarize] %i missing values were ignored.\n", n.bad))
  }
  x
}