Use this if you are using igraph from R
Plot a hierarchical random graph as a dendrogram.
## S3 method for class 'igraphHRG' plot_dendrogram(x, mode = igraph_opt("dend.plot.type"), ...)
x |
An |
mode |
Which dendrogram plotting function to use. See details below. |
... |
Additional arguments to supply to the dendrogram plotting function. |
plot_dendrogram
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:
plot_dendrogram(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"
):
plot_dendrogram(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"
):
plot_dendrogram(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 <- make_full_graph(5) + make_full_graph(5) hrg <- fit_hrg(g) plot_dendrogram(hrg)