dissim.heatmap: Plot Distance Matrix Heatmap for OTU Samples

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

Description

This function consumes an OTU table, along with some optional parameters, and creates a heatmap showing the distance matrix for the samples of the given OTU table.

Usage

dissim.heatmap(data, is.OTU=TRUE, meta=NULL, row.factor=NULL,
               col.factor=NULL, stand.method="chi.square",
               dissim.method="euclidean",
               file=NULL, ext=NULL, height=8, width=9,
               leg.x=-0.05, 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.
row.factor	a factor from the metadata to show along the rows of the heatmap (see Details below).
col.factor	a factor from the metadata to show along the columns of the heatmap (see Details below).
stand.method	a method used to standardize the OTU table. One of "total", "max", "freq", "normalize", "range", "standardize", "pa", "chi.square", "hellinger" or "log" (see ?decostand).
dissim.method	the dissimilarity index to be used; one of "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower","morisita", "horn", "mountford", "raup", "binomial", "chao", or "cao" (see ?vegdist).
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

Both row.factor and col.factor should be named character vectors specifying the names of the rows to be used from meta (see RAM.factors). They should also be factors; if they are not, a warning is raised and they are coerced to factors (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.

Note

This function creates the heatmap using the heatmap.2 function from the gplots package. That function calls layout to set up the plotting environment, which currently prevents plotting two data sets side by side, or to automatically place the (metadata) legend. Unfortunately, this means that the leg.x and leg.y parameters must be used to adjust the legend by trial and error. It is possible to move the legend outside of the plotting area; if not legend appears, try with small leg.x and leg.y values.

Author(s)

Wen Chen and Joshua Simpson.

See Also

decostand, vegdist, factor, heatmap.2, RAM.factors

Examples

data(ITS1, meta)
# plot to the screen with one meta factor and standard
# calculation methods
dissim.heatmap(ITS1, is.OTU=TRUE, meta=meta, 
               row.factor=c(Plot="Plots"))
## Not run: 
# plot the heatmap to a .tiff file using Hellinger 
# standardization and Manhattan distances
dissim.heatmap(ITS1, dissim.method="manhattan",
               stand.method="hellinger",
               file="my/sample/path", ext="tiff")
## End(Not run)

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