plotReads: Function to plot aligned reads along the chromosome

In girafe: Genome Intervals and Read Alignments for Functional Exploration

Description

Function to plot aligned reads along the chromosome

Usage

plotReads(dat, ylim, strand = "plus", vpr, sampleColor = NULL,
   zeroLine = FALSE, main, pointSize = unit(1, "mm"),
   cexAxisLabel = 1, cexAxis = 1, ylab, ...)

Arguments

dat	a list with arguments x.start integer; the genome start coordinates of the data to visualise x.end integer; the genome end coordinates of the data to visualise y numeric; the levels of the data to visualise flag numeric; specifies the category of each value, e.g. marks which data values belong to unique read alignments and which not
ylim	y-axis limits of the plotting window
strand	string; which of the two strands is plotted
vpr	which viewport to use for this plot
sampleColor	which colour to use for the data
zeroLine	logical; should a line at y=0 be drawn?
main	string; main title for the plot
pointSize	width of each dot/bar
cexAxisLabel	numeric; expansion factor for the axis labels
cexAxis	numeric; expansion factor for the axis labels
ylab	y-axis label
...	further arguments passed on to the more primitive plotting functions that are used

Details

This function is used inside the plotting method for objects of class AlignedGenomeIntervals.

Value

returns Null; called for plotting single reads inside the function plotAligned

Author(s)

Joern Toedling

girafe documentation built on Nov. 8, 2020, 4:56 p.m.