RAM (version 1.2.1.3)

factor.abundance: Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank For Each Level of A Metadata Category Variable.

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

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)