get_pca {MicrobiotaProcess} | R Documentation |
Performs a principal components analysis
get_pca(obj, ...) ## S3 method for class 'data.frame' get_pca(obj, sampleda = NULL, method = "hellinger", ...) ## S3 method for class 'phyloseq' get_pca(obj, method = "hellinger", ...)
obj |
phyloseq, phyloseq class or data.frame shape of data.frame is nrow sample * ncol feature. |
... |
additional parameters, see |
sampleda |
data.frame, nrow sample * ncol factors. |
method |
character, the standardization methods for
community ecologists. see |
pcasample class, contained prcomp class and sample information.
# don't run in examples #library(phyloseq) #data(GlobalPatterns) #subGlobal <- subset_samples(GlobalPatterns, # SampleType %in% c("Feces", "Mock", "Ocean", "Skin")) #pcares <- get_pca(subGlobal, method="hellinger") #pcaplot <- ggordpoint(pcares, biplot=TRUE, # speciesannot=TRUE, # factorNames=c("SampleType"), ellipse=TRUE)