Package 'metagenomeSeq' - Bioconductor

plotFeature 37plotFeatureBasic plot function of the raw or normalized data.DescriptionUsageThis function plots the abundance of a particular OTU by class. The function is the typical manhattanplot of the abundances.plotFeature(obj, otuIndex, classIndex, col = "black", sort = TRUE,sortby = NULL, norm = TRUE, log = TRUE, sl = 1000, ...)ArgumentsobjotuIndexclassIndexcolsortsortbynormlogslValueA MRexperiment object with count data.The row to plotA list of the samples in their respective groups.A vector to color samples by.Boolean, sort or not.Default is sort by library size, alternative vector for sortingWhether or not to normalize the counts - if MRexperiment object.Whether or not to log2 transform the counts - if MRexperiment object.Scaling factor - if MRexperiment and norm=TRUE.... Additional plot arguments.NASee AlsocumNormExamplesdata(mouseData)classIndex=list(Western=which(pData(mouseData)$diet=="Western"))classIndex$BK=which(pData(mouseData)$diet=="BK")otuIndex = 8770par(mfrow=c(2,1))dates = pData(mouseData)$dateplotFeature(mouseData,norm=FALSE,log=FALSE,otuIndex,classIndex,col=dates,sortby=dates,ylab="Raw reads")