group.spec: Boxplot Of Richness For Each Level Of A Given Metadata...

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function first use specpool to estimate the extrapolated species richness in a species pool (levels of metadata variable), and the number of unobserved species, then do a boxplot for percent of observed richness.

Usage

group.spec(otu, meta, factor, file=NULL, ext=NULL, 
           width=8,height=8)

Arguments

otu	an OTU table.
meta	the metadata table to be used (must have same samples as data.
factor	a character string. Must be one of the metadata variables.
file	optional. Filename that the plot to be saved to.
ext	optional. Filename extension, type of image to be saved.
width	an integer. Filter OTU table by counts.
height	an integer. Filter OTU table by counts.

Value

This function returns a boxplot of species richness for a given metadata variable.

Author(s)

Wen Chen.

See Also

specpool, specpool

Examples

data(ITS1, meta)
group.spec(ITS1, meta, "Crop")

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: ggplot2
Registered S3 method overwritten by 'ade4':
  method       from  
  summary.dist labdsv
Using Crop, rownames(df.t) as id variables

RAM documentation built on May 2, 2019, 3:04 p.m.