plotOTU {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.
plotOTU(obj, otu, classIndex, log = TRUE, norm = TRUE, jitter.factor = 1, pch = 21, labs = TRUE, xlab = NULL, ylab = NULL, jitter = TRUE, ...)
obj |
A MRexperiment object with count data. |
otu |
The row number/OTU to plot. |
classIndex |
A list of the samples in their respective groups. |
log |
Whether or not to log2 transform the counts - if MRexperiment object. |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
jitter.factor |
Factor value for jitter. |
pch |
Standard pch value for the plot command. |
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. |
... |
Additional plot arguments. |
Plotted values
data(mouseData) classIndex=list(controls=which(pData(mouseData)$diet=="BK")) classIndex$cases=which(pData(mouseData)$diet=="Western") # you can specify whether or not to normalize, and to what level plotOTU(mouseData,otu=9083,classIndex,norm=FALSE,main="9083 feature abundances")