ggrarecurve {MicrobiotaProcess}R Documentation

Rarefaction alpha index

Description

Rarefaction alpha index

Usage

ggrarecurve(obj, ...)

## S3 method for class 'phyloseq'
ggrarecurve(obj, ...)

## Default S3 method:
ggrarecurve(
  obj,
  sampleda,
  indexNames = "Observe",
  linesize = 0.5,
  facetnrow = 1,
  mapping = NULL,
  chunks = 400,
  factorNames,
  factorLevels,
  se = FALSE,
  method = "lm",
  formula = y ~ log(x),
  ...
)

Arguments

obj

phyloseq, phyloseq class or data.frame shape of data.frame (nrow sample * ncol feature (factor)) or ' the data.frame for stat_smooth.

...

additional parameters, see also ggplot2{ggplot}.

sampleda

data.frame, (nrow sample * ncol factor)

indexNames

character, default is "Observe", only for "Observe", "Chao1", "ACE", "Shannon", "Simpson", "J".

linesize

integer, default is 0.5.

facetnrow

integer, the nrow of facet, default is 1.

mapping

set of aesthetic mapping of ggplot2, default is NULL, if the data is the data.frame for stat_smooth, the mapping should be set.

chunks

integer, the number of subsample in a sample, default is 400.

factorNames

character, default is missing.

factorLevels

list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.

se

logical, default is FALSE.

method

character, default is lm.

formula

formula, default is 'y ~ log(x)'

Value

figure of rarefaction curves

Author(s)

Shuangbin Xu

Examples

data(test_otu_data)
library(ggplot2)
prare <- ggrarecurve(test_otu_data,
               indexNames=c("Observe","Chao1","ACE"), 
               chunks=300) +
         theme(legend.spacing.y=unit(0.02,"cm"),
               legend.text=element_text(size=6))

[Package MicrobiotaProcess version 1.0.5 Index]