heatmapp

Plots a heat map with ancestral states.

Usage

heatmapp(x, ...)

# S3 method for class 'phylo'
heatmapp(x, y, use.edge.length = TRUE, align_label = TRUE,
  clade = NULL, select = NULL, cex.lab = 1, nodes = FALSE, ...)

# S3 method for class 'pml'
heatmapp(x, ...)

# S3 method for class 'ancestral'
heatmapp(x, nodes = TRUE, ...)

Arguments

x: an object of class ancestral or phyDat.
...: Further arguments passed to or from other methods.
y: an object of class phyDat.
use.edge.length: a logical indicating whether to use the edge lengths of the phylogeny to draw the branches (the default) or not (if FALSE). This option has no effect if the object of class "phylo" has no ‘edge.length’ element.
align_label: a logical value or an integer. If TRUE, the tips are aligned and dotted lines are drawn between the nodes of the tree and the labels.
clade: a node number or label to extract the clade from the tree.
select: a subset of characters, columns in the alignment.
cex.lab: font size of the labels.
nodes: Show ancestral sequences at internal nodes.

Value

heatmapp returns silently a x

Details

heatmapp plots a heatmap, a phylogeny together with the alignment. For ancestral reconstructions it additionally plots the joint distribution or the most likely state of the internal nodes. This eases comparison of ancestors with related Descendant sequences.

heatmapp is based on the ape function splot.phylo and image.AAbin or image.AAbin.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples

data(woodmouse)
wm <- as.phyDat(woodmouse)
tree <- pratchet(wm)
tree <- makeNodeLabel(tree)
anc_mp <- anc_pars(tree, wm)
op <- par(mar=c(4,1,4,5))
heatmapp(anc_mp)

heatmapp(tree, woodmouse)

par(op)