plotFeature {metagenomeSeq} | R Documentation |
This function plots the abundance of a particular OTU by class. The function is the typical manhattan plot of the abundances.
plotFeature( obj, otuIndex, classIndex, col = "black", sort = TRUE, sortby = NULL, norm = TRUE, log = TRUE, sl = 1000, ... )
obj |
A MRexperiment object with count data. |
otuIndex |
The row to plot |
classIndex |
A list of the samples in their respective groups. |
col |
A vector to color samples by. |
sort |
Boolean, sort or not. |
sortby |
Default is sort by library size, alternative vector for sorting |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
log |
Whether or not to log2 transform the counts - if MRexperiment object. |
sl |
Scaling factor - if MRexperiment and norm=TRUE. |
... |
Additional plot arguments. |
counts and classindex
data(mouseData) classIndex=list(Western=which(pData(mouseData)$diet=="Western")) classIndex$BK=which(pData(mouseData)$diet=="BK") otuIndex = 8770 par(mfrow=c(2,1)) dates = pData(mouseData)$date plotFeature(mouseData,norm=FALSE,log=FALSE,otuIndex,classIndex, col=dates,sortby=dates,ylab="Raw reads")