get_taxadf {MicrobiotaProcess} | R Documentation |
get the data of specified taxonomy
get_taxadf(obj, ...) ## S4 method for signature 'phyloseq' get_taxadf(obj, taxlevel = 2, type = "species", ...) ## S4 method for signature 'data.frame' get_taxadf( obj, taxda, taxa_are_rows, taxlevel, sampleda = NULL, type = "species", ... )
obj |
phyloseq, phyloseq class or data.frame the shape of data.frame (nrow sample * column feature taxa_are_rows set FALSE, nrow feature * ncol sample, taxa_are_rows set TRUE). |
..., |
additional parameters. |
taxlevel |
character, the column names of taxda that you want to get. when the input is phyloseq class, you can use 1 to 7. |
type |
character, the type of datasets, default is "species", if the dataset is not about species, such as dataset of kegg function, you should set it to "others". |
taxda |
data.frame, the classifies of feature contained in obj(data.frame). |
taxa_are_rows |
logical, if the column of data.frame are features, it should be set FALSE. |
sampleda |
data.frame, the sample information. |
phyloseq class contained tax data.frame and sample information.
Shuangbin Xu
## Not run: library(ggplot2) data(test_otu_data) test_otu_data %<>% as.phyloseq() phytax <- get_taxadf(test_otu_data, taxlevel=2) phytax head(phyloseq::otu_table(phytax)) phybar <- ggbartax(phytax) + xlab(NULL) + ylab("relative abundance (%)") ## End(Not run)