get_taxadf: get the data of specified taxonomy

In xiangpin/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

get the data of specified taxonomy

Description

get the data of specified taxonomy

Usage

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",
  ...
)

Arguments

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.

Value

phyloseq class contained tax data.frame and sample information.

Author(s)

Shuangbin Xu

Examples

## 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)

xiangpin/MicrobiotaProcess documentation built on Nov. 12, 2024, 2:05 p.m.