phylobase (version 0.6.8)

treePlot-methods: Phylogeny plotting

Description

Plot phylo4 or phylo4d objects, including associated data.

Usage

## S3 method for class 'phylo4,phylo4d':
treePlot(phy, type = c("phylogram", "cladogram", "fan"), show.tip.label = TRUE, 
  show.node.label = FALSE, tip.order = NULL, plot.data = is(phy, "phylo4d"), 
  rot = 0, tip.plot.fun = "bubbles", edge.color = "black", 
  node.color = "black", tip.color = "black", edge.width = 1, newpage = TRUE, ...)

Arguments

phy

A phylo4 or phylo4d object

type

A character string indicating the shape of plotted tree

show.tip.label

Logical, indicating whether tip labels should be shown

show.node.label

Logical, indicating whether node labels should be shown

tip.order

If NULL the tree is plotted with tips in preorder, if "rev" this is reversed. Otherwise, it is a character vector of tip labels, indicating their order along the y axis (from top to bottom). Or, a numeric vector of tip node IDs indicating the order.

plot.data

Logical indicating whether phylo4d data should be plotted

rot

Numeric indicating the rotation of the plot in degrees

tip.plot.fun

A function used to generate plot at the each tip of the phylogenetic trees

edge.color

A vector of colors in the order of edges(phy)

node.color

A vector of colors indicating the colors of the node labels

tip.color

A vector of colors indicating the colors of the tip labels

edge.width

A vector in the order of edges(phy) indicating the widths of edge lines

newpage

Logical indicating whether the page should be cleared before plotting

...

Currently unused, parameters to be passed on to gpar

Value

• No return value, function invoked for plotting side effect

See Also

phylobubbles

Examples

## example of plotting two grid plots on the same page
data(geospiza)
geotree <- extractTree(geospiza)
grid.newpage()
pushViewport(viewport(layout=grid.layout(nrow=1, ncol=2), name="base"))
  pushViewport(viewport(layout.pos.col=1, name="plot1"))
    treePlot(geotree, newpage=FALSE)
  popViewport()
  
  pushViewport(viewport(layout.pos.col=2, name="plot2"))
    treePlot(geotree, newpage=FALSE, rot=180)
popViewport(2)