treePlot-methods: Phylogeny plotting

In phylobase: Base package for phylogenetic structures and comparative data

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
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
plot.at.tip	should the data plots be at the tip? (logical)
margins	number of lines around the plot (similar to par(mar)).
...	Arguments to be passed to methods, such as graphical parameters (see par). Many methods will accept the following arguments: type what type of plot should be drawn. Possible types are "p" for points, "l" for lines, "b" for both, "c" for the lines part alone of "b", "o" for both ‘overplotted’, "h" for ‘histogram’ like (or ‘high-density’) vertical lines, "s" for stair steps, "S" for other steps, see ‘Details’ below, "n" for no plotting. All other types give a warning or an error; using, e.g., type = "punkte" being equivalent to type = "p" for S compatibility. Note that some methods, e.g. plot.factor, do not accept this. main an overall title for the plot: see title. sub a sub title for the plot: see title. xlab a title for the x axis: see title. ylab a title for the y axis: see title. asp the y/x aspect ratio, see plot.window.
x	the coordinates of points in the plot. Alternatively, a single plotting structure, function or any R object with a plot method can be provided.
y	the y coordinates of points in the plot, optional if x is an appropriate structure.

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]

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)

phylobase documentation built on May 2, 2019, 6:49 p.m.