group.abundance: Plot the Abundance of OTUs by Classification at a Given...

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

Description

This function consumes an OTU, and a rank, as well as various optional parameters. It creates a stacked bar plot showing the abundance of all classifications at the given taxonomic rank for each sample.

Usage

group.abundance(data, rank,
                top=NULL, count=FALSE, drop.unclassified=FALSE,
                cex.x=NULL, main=NULL, file=NULL, ext=NULL,
                height=8, width=16, bw=FALSE, ggplot2=TRUE)

Arguments

data	a list of OTU tables.
rank	the taxonomic rank to use. See RAM.rank.formatting.
top	the number of groups to select, starting with the most abundant. If NULL, all are selected.
count	logical. If TRUE, the numerical counts for each OTU will be shown; otherwise the relative abundance will be shown.
drop.unclassified	logical. Should unclassified samples be excluded from the data?
cex.x	optional. The size of x axis names.
main	the title of the plot
file	the file path where the image should be created (see ?RAM.plotting).
ext	the file type to be used; one of "pdf", "png", "tiff", "bmp", "jpg", or "svg".
height	the height of the image to be created (in inches).
width	the width of the image to be created (in inches).
bw	logical. Should the image be created in black and white?
ggplot2	logical. Should the ggplot2 package be used to produce the plot, or should the base graphics be used? (see ?RAM.plotting).

Author(s)

Wen Chen and Joshua Simpson

Examples

data(ITS1, ITS2)
# plot the relative abundance at the class level to the screen, 
# ignoring the unclassified
group.abundance(data=list(ITS1=ITS1), rank="phylum",
                drop.unclassified=TRUE)
## Not run: 
# plot the count abundance at the phylum level to path.tiff
group.abundance(data=list(ITS1=ITS1, ITS2=ITS2), rank="g",
                top=10, count=FALSE, drop.unclassified=TRUE,
                main="", file=NULL, ext=NULL,
                height=8, width=16, bw=FALSE, ggplot=TRUE)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied

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