RAM (version 1.2.0)

group.heatmap.simple: Plot a Heatmap Showing OTU Abundance by Taxonomic Classification

Description

This function consumes an OTU table and a rank, as well as some optional parameters, and creates a heatmap showing the abundance of the OTUs at the given taxonomic rank for each sample.

Usage

group.heatmap.simple(data, is.OTU=TRUE, meta=NULL, rank, row.factor=NULL,
                     top=NULL, count=FALSE, drop.unclassified=FALSE,
                     dendro="none", file=NULL, ext=NULL, 
                     width=9, height=8, leg.x=-0.08, leg.y=0)

Arguments

data

the OTU table to be used.

is.OTU

logical. Whether or not the data is an OTU table.

meta

the metadata table to be used.

rank

the taxonomic rank to use (see ?RAM.rank.formatting for formatting details).

row.factor

a factor from the metadata to show along the rows of the heatmap. (see Details below).

dendro

a character vector specifying on which axes (if any) a dendrogram should be plotted. Must be one of "none", "both", "column", or "row".

top

the number of groups to select, starting with the most abundant. If NULL, all are selected.

count

logical. Should the actual count of each OTU be shown, or should the relative abundances be shown?

drop.unclassified

logical. Should OTUs labelled "unclassified" or missing classification at the given taxonomic rank be excluded?

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).

leg.x

how far the legend should be inset, on the x axis.

leg.y

how far the legend should be inset, on the y axis.

Details

row.factor should be a named character vector specifying the name of the row to be used from meta (see RAM.factors). It should also be a factor; if it is not, a warning is raised and it is coerced to a factor (see factor). A warning is also raised when a factor has more than 8 levels, as that is the most colours the current palettes support. The factor must also correspond to the OTU table; i.e. they should have the same samples. If not, an error is raised.

See Also

factor, heatmap.2, RAM.factors

Examples

data(ITS1, meta)

# plot the abundance of all observed classes for each sample, displaying 
# it to the screen and adding a dendrogram on the column and the Collector 
# on the row 
group.heatmap.simple(ITS1, is.OTU=TRUE, meta=meta, 
                     row.factor=c(Crop="Crop"), dendro="row", 
                     rank="g", top=10, drop.unclassified=TRUE, 
                     leg.x=-0.06)

# plot the genus for all OTUs, add a dendrogram to the row and column, 
# and save the plot in path.tiff
group.heatmap.simple(ITS1, is.OTU=TRUE, meta=meta, rank="genus", 
                     dendro="both", file="my/file/path")