ggrarecurve: Rarefaction alpha index

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

Rarefaction alpha index

Description

Rarefaction alpha index

Usage

ggrarecurve(obj, ...)

## S3 method for class 'phyloseq'
ggrarecurve(obj, chunks = 400, factorLevels = NULL, ...)

## S3 method for class 'data.frame'
ggrarecurve(obj, sampleda, factorLevels, chunks = 400, ...)

## S3 method for class 'rarecurve'
ggrarecurve(
  obj,
  indexNames = "Observe",
  linesize = 0.5,
  facetnrow = 1,
  shadow = TRUE,
  factorNames,
  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)).
...	additional parameters, see also ggplot2{ggplot}.
chunks	integer, the number of subsample in a sample, default is 400.
factorLevels	list, the levels of the factors, default is NULL, if you want to order the levels of factor, you can set this.
sampleda	data.frame, (nrow sample * ncol factor)
indexNames	character, default is "Observe", only for "Observe", "Chao1", "ACE".
linesize	integer, default is 0.5.
facetnrow	integer, the nrow of facet, default is 1.
shadow	logical, whether merge samples with group (factorNames) and display the ribbon of group, default is TRUE.
factorNames	character, default is missing.
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

## Not run: 
data(test_otu_data)
test_otu_data %<>% as.phyloseq()
library(ggplot2)
prare <- ggrarecurve(test_otu_data,
               indexNames=c("Observe","Chao1","ACE"),
               shadow=FALSE,
               factorNames="group"
         ) +
         theme(legend.spacing.y=unit(0.02,"cm"),
               legend.text=element_text(size=6))

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.