sequenza (version 1.0.5)

plotWindows: Plot the specified windowed chromosome.

Description

plotWindows is a convenient plot function that visualizes a specified chromosome attribute using the matrix produced by the function windowValues.

Usage

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

Arguments

abf.window

matrix of base-pair windows and corresponding statistics to be plotted. A list of such matrices can be output from windowValues

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

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

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