ChemoSpec (version 4.3.34)

hmapSpectra: Create a Seriated Heat Map Comparing Samples and Spectral Data for a Spectra Object

Description

Creates a heat map with marginal dendrograms using seriation procedures. Very briefly, the samples that are most like each other occur in one corner, and the frequencies that are most informative with respect to the samples are in that corner as well. This is achieved by using heirchical cluster analysis and then re-ordering the clusters in a coordinated way across each dimension. See the vignette for package seriation.

Usage

hmapSpectra(spectra, ...)

Arguments

spectra

An object of S3 class Spectra.

...

Additional arguments to be passed downstream. A great deal of control is available - check ?hmap for details. Most of the control actually derives from the heatmap2 function in package gplots.

Value

A list composed of two data frames. One is the frequencies and their rankings, the other is samples and their rankings. Side effect is a plot.

References

https://github.com/bryanhanson/ChemoSpec

See Also

hmap which will get you to the package (there is no package index page); the vignette is a good place to begin (browseVignettes("seriation")).

Examples

data(SrE.IR)
# Let's look just at the carbonyl region
IR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 1850 | SrE.IR$freq < 1650)
res <- hmapSpectra(IR, col = heat.colors(5), labCol = FALSE)