group.heatmap: Plot OTU Abundance at a Given Rank with Metadata Annotation

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function plots the abundance for all taxon groups at a given rank. Additionally, it can display metadata for the samples as annotations along the rows of the heatmap.

Usage

group.heatmap(data, is.OTU=TRUE, meta, rank, factors,
              top=25, remove.unclassified=TRUE,
              stand.method=NULL,
              dist.method="bray",
              hclust.method="average",
              dendro.row.status="yes",
              dendro.col.status="hidden",
              row.labels=TRUE, row.cex=1,
              cut=NULL, file=NULL, ext=NULL,
              width=9, height=9)

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).
factors	a named character vector indicating the columns of the metadata table to be used (see RAM.factors).
top	the number of groups to select, starting with the most abundant. If NULL, all are selected.
remove.unclassified	logical. Define whether OTUs labelled "unclassified" or missing classification at the given taxonomic rank should be excluded.
stand.method	optional. Data standardization methods specified in decostand.
dist.method	distance matrix calculation methods specified vegdist.
hclust.method	the agglomeration methods specified in hclust. This should be unambiguous abbreviation of one of the following: 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'.
dendro.row.status	whether or not to use the dendrogram to re-order the rows. It should be one of the following: 'yes' that use the dendrogram to re-order the rows/columns and display the dendrogram; 'hidden' means re-rorder, but do not display; 'no' means do not use the dendrogram at all. See also annHeatmap2
dendro.col.status	whether or not to use the dendrogram to re-order the columns. It should be one of the following: 'yes' that use the dendrogram to re-order the rows/columns and display the dendrogram; 'hidden' means re-rorder, but do not display; 'no' means do not use the dendrogram at all. See also annHeatmap2
row.labels	logical. Whether or not to plot the row labels.
row.cex	the size of row labels if row.labels is TRUE
cut	the height at which to cut the sample tree, this will create distinct coloured groups. Currently this will allow for at most nine groups (see Details).
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).

Details

A warning from brewer.pal indicating "n too large, allowed maximum for palette Pastel1 is 9" means that the cut height is too low to allow for that many groups. This should be fixed in a future release.

Author(s)

Wen Chen and Joshua Simpson.

See Also

decostand, annHeatmap2

Examples

data(ITS1, meta)
## Not run: 
#library("Heatplus")
#library("RColorBrewer")
#group.heatmap(ITS1, is.OTU=TRUE, meta=meta, rank="c", 
              factors=c(Crop="Crop", City="City"), 
              stand.method="chi", dist.method="euc",
              hclust.method="mcquitty", cut=0.5)
#
## End(Not run)

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