gl.plot.heatmap: Represents a distance matrix as a heatmap

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Represents a distance matrix as a heatmap

Description

The script plots a heat map to represent the distances in the distance or dissimilarity matrix. This function is a wrapper for heatmap.2 (package gplots).

Usage

gl.plot.heatmap(D, palette_divergent = diverging_palette, verbose = NULL, ...)

Arguments

D	Name of the distance matrix or class fd object [required].
palette_divergent	A divergent palette for the distance values [default diverging_palette].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]
...	Parameters passed to function heatmap.2 (package gplots)

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr)

Examples

## Not run: 
   gl <- testset.gl[1:10,]
   D <- dist(as.matrix(gl),upper=TRUE,diag=TRUE)
   gl.plot.heatmap(D)
   D2 <- gl.dist.pop(possums.gl)
   gl.plot.heatmap(D2)
   D3 <- gl.fixed.diff(testset.gl)
   gl.plot.heatmap(D3)
   
## End(Not run)
   if ((requireNamespace("gplots", quietly = TRUE))) {
   D2 <- gl.dist.pop(possums.gl)
   gl.plot.heatmap(D2)
   }

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.