plotWindows: Plot a binned values of a chromosome

In sequenza: Copy Number Estimation from Tumor Genome Sequencing Data

Description

The plotWindows function visualizes a data.frame produced by the windowValues or windowBf functions.

Usage

plotWindows(seqz.window, m.lty = 1, m.lwd = 3, m.col = "black",
    q.bg = "lightblue", log2.plot = FALSE, n.min = 1, xlim, ylim,
    add = FALSE, ...)

Arguments

seqz.window	data frame of base-pair windows and corresponding quartiles to be plotted. A list of such data frames can be output from windowValues or windowBf.
m.lty	line type used for plotting mean values.
m.lwd	line width used for plotting mean values.
m.col	line color used for plotting mean values.
q.bg	background color for the area between the 0.25 and 0.75 quartiles.
log2.plot	logical, if TRUE values are log2 scaled.
n.min	minimum number of data points required for a binned window to be plotted.
xlim	limits of the x axis.
ylim	limits of the y axis.
add	logical, if TRUE the plot will be added to an existing opened device.
...	any other arguments accepted by plot.

See Also

chromosome.view,

Examples

    data.file <-  system.file("extdata", "example.seqz.txt.gz",
        package = "sequenza")
    seqz.data <- read.seqz(data.file)
    # 1Mb windows, each window is overlapping with 1 other adjacent
    # window: depth ratio
    seqz.ratio <- windowValues(x = seqz.data$depth.ratio,
        positions = seqz.data$position, chromosomes = seqz.data$chromosome,
        window = 1e6, weight = seqz.data$depth.normal, start.coord = 1,
        overlap = 1)

    plotWindows(seqz.ratio[[1]], log2.plot = FALSE, ylab = "Depth ratio",
        xlab = "Position (bases)", main = names(seqz.ratio)[1], las = 1,
        n.min = 1, ylim = c(0, 2.5))

    plotWindows(seqz.ratio[[17]], log2.plot = FALSE, ylab = "Depth ratio",
        xlab = "Position (bases)", main = names(seqz.ratio)[1], las = 1,
        n.min = 1, ylim = c(0, 2.5))

Example output

sequenza documentation built on May 9, 2019, 5:04 p.m.