get_rarecurve {MicrobiotaProcess} | R Documentation

## obtain the result of rare curve

### Description

generate the result of rare curve.

### Usage

    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, ...)

### Arguments

`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.

### Details

This function is designed to calculate the rare curve result of otu table the result can be visualized by 'ggrarecurve'.

### Value

rarecurve class, which can be visualized by ggrarecurve

### Author(s)

Shuangbin Xu

### Examples

    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")

[Package MicrobiotaProcess version 1.2.2 Index]