treePlot-methods: Phylogeny plotting

In phylobase: Base Package for Phylogenetic Structures and Comparative Data

Phylogeny plotting

Description

Plot phylo4 or phylo4d objects, including associated data.

Usage

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",
  plot.at.tip = TRUE,
  edge.color = "black",
  node.color = "black",
  tip.color = "black",
  edge.width = 1,
  newpage = TRUE,
  margins = c(1.1, 1.1, 1.1, 1.1),
  ...
)

plot(x, y, ...)

## S4 method for signature 'phylo4,missing'
plot(x, y, ...)

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
plot.at.tip	should the data plots be at the tip? (logical)
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
margins	number of lines around the plot (similar to par(mar)).
...	additional arguments
x	A phylo4 or phylo4d object
y	(only here for compatibility)

Details

Currently, treePlot can only plot numeric values for tree-associated data. The dataset will be subset to only include columns of class numeric, integer or double. If a phylo4d object is passed to the function and it contains no data, or if the data is in a format that cannot be plotted, the function will produce a warning. You can avoid this by using the argument plot.data=FALSE.

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 [e-mail], Francois Michonneau

See Also

phylobubbles

Examples

## example of plotting two grid plots on the same page
library(grid)
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)

phylobase documentation built on May 29, 2024, 11:24 a.m.