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
## Not run: 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") ## End(Not run)