plotOrd {metagenomeSeq} | R Documentation |
This function plots the PCA / MDS coordinates for the "n" features of interest. Potentially uncovering batch effects or feature relationships.
plotOrd( obj, tran = TRUE, comp = 1:2, norm = TRUE, log = TRUE, usePCA = TRUE, useDist = FALSE, distfun = stats::dist, dist.method = "euclidian", n = NULL, ... )
obj |
A MRexperiment object or count matrix. |
tran |
Transpose the matrix. |
comp |
Which components to display |
norm |
Whether or not to normalize the counts - if MRexperiment object. |
log |
Whether or not to log2 the counts - if MRexperiment object. |
usePCA |
TRUE/FALSE whether to use PCA or MDS coordinates (TRUE is PCA). |
useDist |
TRUE/FALSE whether to calculate distances. |
distfun |
Distance function, default is stats::dist |
dist.method |
If useDist==TRUE, what method to calculate distances. |
n |
Number of features to make use of in calculating your distances. |
... |
Additional plot arguments. |
coordinates
data(mouseData) cl = pData(mouseData)[,3] plotOrd(mouseData,tran=TRUE,useDist=TRUE,pch=21,bg=factor(cl),usePCA=FALSE)