treePlot-methods {phylobase}R Documentation

Phylogeny plotting

Description

Plot phylo4 or phylo4d objects, including associated data.

Usage

  ## S4 method for signature '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 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

Methods

phy = "phylo4"
plots a tree of class phylo4
phy = "phylo4d"
plots a tree with one or more quantitative traits contained in a phylo4d object.

Author(s)

Peter Cowan pdc@berkeley.edu

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)


[Package phylobase version 0.5 Index]