plotRare: Plot of rarefaction effect

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Plot of rarefaction effect

Description

This function plots the number of observed features vs. the depth of coverage.

Usage

plotRare(obj, cl = NULL, ...)

Arguments

obj	A MRexperiment object with count data or matrix.
cl	Vector of classes for various samples.
...	Additional plot arguments.

Value

Library size and number of detected features

See Also

plotOrd, plotMRheatmap, plotCorr, plotOTU, plotGenus

Examples

data(mouseData)
cl = factor(pData(mouseData)[,3])
res = plotRare(mouseData,cl=cl,pch=21,bg=cl)
tmp=lapply(levels(cl), function(lv) lm(res[,"ident"]~res[,"libSize"]-1, subset=cl==lv))
for(i in 1:length(levels(cl))){
   abline(tmp[[i]], col=i)
}
legend("topleft", c("Diet 1","Diet 2"), text.col=c(1,2),box.col=NA)

HCBravoLab/metagenomeSeq documentation built on Dec. 20, 2024, 4:06 p.m.