plotCoverage: Plots a genome-browser-like image of a region

In MatthiasLienhard/qsea: IP-seq data analysis and vizualization

Plots a genome-browser-like image of a region

Description

This function plots the normalized coverage of specified samples in a specified region, together with annotations, in a genome-browser-like fashion

Usage

plotCoverage(qs,test_results, chr, start, end, samples,samples2, 
norm_method="nrpkm", yoffset, xlab="Position", 
ylab="MeDIP seq", col="black", main, reorder="non", indicate_reorder=TRUE, 
distfun=dist, clustmethod="complete", scale=TRUE, steps=TRUE, space=0.05, 
baselines=TRUE, scale_val, scale_unit=NULL, logFC_pc=.1, cex=1, smooth_width, 
smooth_function=mean, regions, regions_lwd=1, regions_col, 
regions_offset, regions_names, regions_dash=0.1)

Arguments

qs	a qseaSet object
chr	the chromosome of the region to be depicted
start	the start position of the region to be depicted
end	the end position of the region to be depicted
samples	the indices of the samples to be depicted
samples2	if specified, used to calculated logFC (samples/samples2) profiles, must be of same length as samples
logFC_pc	if samples2 is specified and logFC are calculated, this parameter specifies the pseudocount to avoid division by zero
norm_method	a vector of normalization methods to be combined
yoffset	horizontal offset, used to adjust the space between the profiles
xlab	title for the x axis
ylab	title for the y axis
main	an overall title for the plot
col	color vector for the samples (is recycled)
reorder	indicate whether, and if yes how, the samples are reordered. Valid values are "non", "clust", "max", "minP", or a genomic position within the range that is depicted
test_results	a qseaGLM object, used to find the region with minimal p value (only if reorder="minP")
indicate_reorder	indicate the window that has been used for reordering by an arrow.
distfun	if reorder="clust": for hierarchical clustering for reordering
clustmethod	if reorder="clust": for hierarchical clustering for reordering
scale	if set TRUE, print a bar scale
scale_val	length of the bar scale
scale_unit	unit of the bar scale
steps	plot the coverage as step function (steps=TRUE), or as lines
space	fraction of the plot set aside for sample names etc.
baselines	depict the baselines (zero) of the coverage profiles
cex	font size
smooth_width	number of windows to be considered for sliding window smoothing
smooth_function	function to be applied on the sliding windows for smoothing
regions	named list of GenomicRanges objects, containing annotation (eg exons) to be depicted below the coverage profiles
regions_lwd	vector of line width for the
regions_col	vector of colors for the regions
regions_offset	offset value, defining the space between the regions
regions_names	vector of column names, that store the names of the regions
regions_dash	vector, specifying the length of the end dashes of the regions

Value

list containing a table containing the plotted coverage values, the position that has been used for ordering, and the image coordinates

Author(s)

Mathias Lienhard

Examples

qs=getExampleQseaSet(repl=5)
colors=c(rep("red", 5), rep("green", 5))
plot(1)
plotCoverage(qs,samples=getSampleNames(qs), 
    chr="chr1", start=1960001, end=1970001,col=colors, 
    norm_method="beta", yoffset=1,space=.2, reorder=1964500)
plotCoverage(qs,samples=getSampleNames(qs), 
    chr="chr1", start=1960001, end=1970001,col=colors, 
    norm_method="beta", yoffset=1,space=.2, reorder="clust")

MatthiasLienhard/qsea documentation built on March 22, 2023, 1:15 p.m.