Phylogeny plotting

Description

Plot phylo4 or phylo4d objects, including associated data.

Usage

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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)).

x

A phylo4 or phylo4d object

y

(only here for compatibility)

...

additional arguments

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 pdc@berkeley.edu, Francois Michonneau

See Also

phylobubbles

Examples

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## 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)

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