plotAB {compartmap} | R Documentation

## Plots A/B compartment estimates on a per chromosome basis

### Description

Plot A/B compartments bins

### Usage

    plotAB(x, main = "", ylim = c(-1, 1), unitarize = FALSE,
      reverse = FALSE, top.col = "deeppink4", bot.col = "grey50")

### Arguments

`x` | The matrix obejct returned from getCompartments
`main` | Title for the plot
`ylim` | Y-axis limits (default is -1 to 1)
`unitarize` | Should the data be unitarized? (not explicitly necessary for arrays)
`reverse` | Reverse the sign of the PC values?
`top.col` | Top (pos. PC values) chromatin color to be plotted
`bot.col` | Bottom (neg. PC values) chromatin color to be plotted

### Value

invisibly, the compartment estimates from the plot

### 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$start <- apply(random_genomic_int, 1, function(x) { round(runif(1, 0, seqlengths(Homo.sapiens)[x][[1]]), 0) })
    random_genomic_int$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)

    ## Not run:
    #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")

    ## End(Not run)

[Package compartmap version 1.0.3 Index]