Description Usage Arguments Value Methods Author(s) See Also Examples
Plot phylo4
or phylo4d
objects, including associated data.
1 2 3 4 5 6 7 8 9 10 11 | 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, ...)
|
phy |
A |
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 |
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 |
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 |
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 |
... |
Arguments to be passed to methods, such as
graphical parameters (see
|
x |
the coordinates of points in the plot. Alternatively, a
single plotting structure, function or any R object with a
|
y |
the y coordinates of points in the plot, optional
if |
No return value, function invoked for plotting side effect
plots a tree of class phylo4
plots a tree with one or more quantitative traits contained in a phylo4d object.
Peter Cowan pdc@berkeley.edu
1 2 3 4 5 6 7 8 9 10 11 12 | ## 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)
|
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