factor.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 level of a metadata category variable.

Usage

factor.abundance(data, rank, top=NULL, count=FALSE, 
                 meta=meta, meta.factor="", 
                 drop.unclassified=FALSE, file=NULL, 
                 ext=NULL, height=8, width=16, main="")

Arguments

data	a list of OTU tables with names.
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.
meta	metadata.
meta.factor	a category variable in metadata
drop.unclassified	logical. Should unclassified samples be excluded from the data?
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).
main	the title of the plot

Author(s)

Wen Chen

Examples

data(ITS1, ITS2, meta)
data=list(ITS1=ITS1, ITS2=ITS2)
# plot the relative abundance at the class level to the screen,
# ignoring the unclassified
factor.abundance(data=data, rank="family", meta=meta,
                 meta.factor=c("Crop"), top=20,
                 drop.unclassified=TRUE)
## Not run: 
# plot the count abundance at the phylum level to path.tiff
factor.abundance(data=data, rank="family", meta=meta,
                 meta.factor=c("Crop"), top=20, count=FALSE,
                 drop.unclassified=TRUE, main="",
                 file="path/to/tiff", ext="tiff", 
                 height=8, width=12)

## End(Not run)

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