RAM (version 1.2.1.3)

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

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.

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)