plotCoverage: Plots a genome-browser-like image of a region
In qsea: IP-seq data analysis and vizualization

Description Usage Arguments Value Author(s) Examples

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

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)

`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

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

Mathias Lienhard

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")