Rgb (version 1.5.1)

draw.pileup:

Description

This function draws a slice of a sequence pileup, highlighting polymorphisms.

Usage

draw.pileup(slice, start, end, ylim = NA, bty = "o", label = TRUE, labelCex = 0.75,
    bases = c(A = "#44CC44", C = "#4444CC", G = "#FFCC00", T = "#CC4444"),
    maxRange = 500, cex.lab = 1, alphaOrder = 3, alphaMin = 0.1, ...)

Arguments

slice
An integer matrix of read counts, with nucleotides in rows and positions in columns. Both dimensions must be named.
start
Single integer value, the left boundary of the window, in base pairs.
end
Single integer value, the right boundary of the window, in base pairs.
ylim
See plot.default. NA will compute a dynamic ylim fiting the data.
bty
A character string which determined the type of box which is drawn about plots. If bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box. See par.
label
Single logical value, whether to print nucleotide on bars or not.
labelCex
Single numeric value, character expansion factor for labels.
bases
Named character vector, defining the color to use for each nucleotide.
maxRange
Single integer value, nothing will be ploted if the plot window is wider by this value (in bases).
cex.lab
The relative character size of x and y axis labels (default: 1). See par.
alphaOrder
Single numeric value, the order of the formula controlling the transparency. Increase this value to increase sensitivity to rare variants.
alphaMin
Single numeric value, the minimal intensity in the formula controlling the transparency (between 0 and 1). Perfectly homozyguous positions will typically use this intensity of color.
Further arguments to be passed to draw.bg.

See Also

track.bam-class draw.bg, draw.boxes, draw.steps, draw.hist, draw.points, draw.seq