Package 'metagenomeSeq' - Bioconductor

42 plotRareplotRarePlot of rarefaction effectDescriptionThis function plots the number of observed features vs. the depth of coverage.UsageplotRare(obj, cl = NULL, ret = FALSE, ...)ArgumentsobjclretA MRexperiment object with count data or matrix.Vector of classes for various samples.True/False, return the number of features and the depth of coverage as a vector.... Additional plot arguments.ValueNASee AlsoplotOrd, plotMRheatmap, plotCorr, plotOTU, plotGenusExamplesdata(mouseData)cl = factor(pData(mouseData)[,3])res = plotRare(mouseData,cl=cl,ret=TRUE,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)