RAM (version 1.2.1.3)

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

Description

This function is an updated version of group.abundance, which groups samples by metadata category variables if provided.

Usage

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

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?

meta

optional, associated metadata of the otu tables, sampleIDs and their orders in otu tables should be identical to those in metadata

meta.factor

optional, category variables in meta

Examples

data(ITS1, ITS2, meta)
## Not run: 
# # plot the relative abundance at the class level to the screen, 
# # drop unclassified taxa
# group.abundance.meta(data, top=10, rank="family", 
#                     drop.unclassified=TRUE, meta=meta, 
#                     meta.factor=c("Year", "Crop", "City"))
# ## End(Not run)