RAM (version 1.2.0)

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

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).

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)

# 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)