plotGenus {metagenomeSeq} | R Documentation |
This function plots the abundance of a particular OTU by class. The function uses the estimated posterior probabilities to make technical zeros transparent.
plotGenus(obj, otuIndex, classIndex, norm = TRUE, log = TRUE, no = 1:length(otuIndex), labs = TRUE, xlab = NULL, ylab = NULL, jitter = TRUE, jitter.factor = 1, pch = 21, ...)
obj |
An MRexperiment object with count data. |
otuIndex |
A list of the otus with the same annotation. |
classIndex |
A list of the samples in their respective groups. |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
log |
Whether or not to log2 transform the counts - if MRexperiment object. |
no |
Which of the otuIndex to plot. |
labs |
Whether to include group labels or not. (TRUE/FALSE) |
xlab |
xlabel for the plot. |
ylab |
ylabel for the plot. |
jitter |
Boolean to jitter the count data or not. |
jitter.factor |
Factor value for jitter |
pch |
Standard pch value for the plot command. |
... |
Additional plot arguments. |
plotted data
data(mouseData) classIndex=list(controls=which(pData(mouseData)$diet=="BK")) classIndex$cases=which(pData(mouseData)$diet=="Western") otuIndex = grep("Strep",fData(mouseData)$family) otuIndex=otuIndex[order(rowSums(MRcounts(mouseData)[otuIndex,]),decreasing=TRUE)] plotGenus(mouseData,otuIndex,classIndex,no=1:2,xaxt="n",norm=FALSE,ylab="Strep normalized log(cpt)")