get_rarecurve {MicrobiotaProcess} | R Documentation |
generate the result of rare curve.
get_rarecurve(obj, ...) ## S4 method for signature 'data.frame' get_rarecurve(obj, sampleda, factorLevels = NULL, chunks = 400) ## S4 method for signature 'phyloseq' get_rarecurve(obj, ...)
obj |
phyloseq class or data.frame shape of data.frame (nrow sample * ncol feature) |
..., |
additional parameters. |
sampleda |
data.frame, (nrow sample * ncol factor) |
factorLevels |
list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this. |
chunks |
integer, the number of subsample in a sample, default is 400. |
This function is designed to calculate the rare curve result of otu table the result can be visualized by 'ggrarecurve'.
rarecurve class, which can be visualized by ggrarecurve
Shuangbin Xu
data(test_otu_data) set.seed(1024) res <- get_rarecurve(test_otu_data, chunks=200) p <- ggrarecurve(obj=res, indexNames=c("Observe","Chao1","ACE"), shadow=FALSE, factorNames="Group")