spider (version 1.2-0)

heatmapSpp: Visualise a distance matrix using a heatmap

Description

This function plots a heatmap of the distance matrix, with shorter distances indicated by darker colours.

Usage

heatmapSpp(distObj, sppVector, col = NULL, axisLabels = NULL)

Arguments

distObj

A matrix or object of class dist.

sppVector

The species vector. See sppVector.

col

A vector giving the colours for the heatmap.

axisLabels

A character vector that provides the axis labels for the heatmap. By default the species vector is used.

Value

• Plots a heatmap of the distance matrix. Darker colours indicate shorter distances, lighter colours indicate greater distances.

Details

The default palette has been taken from the colorspace package.

Examples

data(dolomedes)
doloDist <- dist.dna(dolomedes, model = "raw")
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)
heatmapSpp(doloDist, doloSpp)
heatmapSpp(doloDist, doloSpp, axisLabels = dimnames(dolomedes)[[1]])

data(anoteropsis)
anoDist <- dist.dna(anoteropsis, model = "raw")
anoSpp <- sapply(strsplit(dimnames(anoteropsis)[[1]], split="_"), 
    function(x) paste(x[1], x[2], sep="_"))
heatmapSpp(anoDist, anoSpp)