treePlot-methods {phylobase} | R Documentation |
Plot phylo4
or phylo4d
objects, including associated data.
## 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, ...)
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 |
No return value, function invoked for plotting side effect
Peter Cowan pdc@berkeley.edu
## 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)