plotEnrichmentProfile: Plotting functions for enrichment profiles

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

Plotting functions for enrichment profiles

Description

Plots the estimated sequence pattern dependent enrichment profile for one or several samples as a matrix of plots

Usage

plotEnrichmentProfile(qs,sample, sPoints=seq(0,30,1), 
    fitPar=list(lty=2, col="green"),cfPar=list(lty=1), densityPar, meanPar,... )
plotEPmatrix(qs, sa=getSampleNames(qs),nrow=ceiling(sqrt(length(sa))), 
    ncol=ceiling(length(sa)/nrow), ...)

Arguments

qs	The qseaSet object
sample	The index of the sample for which the enrichment profile should be depicted
sPoints	The values at which the enrichment profile function is evaluated
fitPar	List of parameters for depiction of the fitted enrichment profile function (see details)
cfPar	List of parameters for depiction of the empirical enrichment profile (see details)
densityPar	List of parameters for depiction high density scatterplot of coverage and pattern density (see details)
meanPar	List of parameters for depiction of the mean coverage per pattern density bin (see details)
sa	vector of samples to be depicted in matrix plot
nrow	number of rows in matrix plot
ncol	number of columns in matrix plot
...	Further graphical parameters may also be supplied

Details

Parameter lists for lines in the plot (e.g. fitPar, cfPar and meanPar) are passed to graphics::lines(), densityPar are passed to graphics::smoothScatter() function.

Value

plotEnrichmentProfile returns the coordinates of the enrichment profile. plotEPmatrix returns enrichment profile coordinates for all depicted samples.

Author(s)

Mathias Lienhard

See Also

addEnrichmentParameters

Examples

#create example object with different sequencing depth
qs=getExampleQseaSet(expSamplingDepth=50*10^(1:4), repl=4)
#enrichment profile for one sample
plotEnrichmentProfile(qs, "Sim4T")
#enrichment profile for all samples
plotEPmatrix(qs)

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