| dendPlot.igraphHRG {igraph} | R Documentation |
Plot a hierarchical random graph as a dendrogram.
## S3 method for class 'igraphHRG'
dendPlot(x, mode = getIgraphOpt("dend.plot.type"),
...)
x |
An |
mode |
Which dendrogram plotting function to use. See details below. |
... |
Additional arguments to supply to the dendrogram plotting function. |
dendPlot supports three different plotting functions, selected
via the mode argument. By default the plotting function is
taken from the dend.plot.type igraph option, and it has for
possible values:
auto Choose automatically between the plotting
functions. As plot.phylo is the most sophisticated, that is
choosen, whenever the ape package is available. Otherwise
plot.hclust is used.
phylo Use plot.phylo from the ape
package.
hclust Use plot.hclust from the stats
package.
dendrogram Use plot.dendrogram from the
stats package.
The different plotting functions take different sets of
arguments. When using plot.phylo (mode="phylo"), we have
the following syntax:
dendPlot(x, mode="phylo",
colbar = rainbow(11, start=0.7, end=0.1),
edge.color = NULL, use.edge.length = FALSE, \dots)
The extra arguments not documented above:
colbar Color bar for the edges.
edge.color Edge colors. If NULL, then the
colbar argument is used.
use.edge.length Passed to plot.phylo.
dots Attitional arguments to pass to
plot.phylo.
The syntax for plot.hclust (mode="hclust"):
dendPlot(x, mode="hclust", rect = 0, colbar = rainbow(rect),
hang = 0.01, ann = FALSE, main = "", sub = "", xlab = "",
ylab = "", \dots)
The extra arguments not documented above:
rect A numeric scalar, the number of groups to mark on
the dendrogram. The dendrogram is cut into exactly rect
groups and they are marked via the rect.hclust command. Set
this to zero if you don't want to mark any groups.
colbar The colors of the rectanges that mark the
vertex groups via the rect argument.
hang Where to put the leaf nodes, this corresponds to the
hang argument of plot.hclust.
ann Whether to annotate the plot, the ann argument
of plot.hclust.
main The main title of the plot, the main argument
of plot.hclust.
sub The sub-title of the plot, the sub argument
of plot.hclust.
xlab The label on the horizontal axis, passed to
plot.hclust.
ylab The label on the vertical axis, passed to
plot.hclust.
dots Attitional arguments to pass to plot.hclust.
The syntax for plot.dendrogram (mode="dendrogram"):
dendPlot(x, \dots)
The extra arguments are simply passed to as.dendrogram.
Returns whatever the return value was from the plotting function,
plot.phylo, plot.dendrogram or plot.hclust.
Gabor Csardi csardi.gabor@gmail.com
g <- graph.full(5) + graph.full(5) hrg <- hrg.fit(g) dendPlot(hrg)