Community structure dendrogram plots
Plot a hierarchical community structure as a dendrogram.
plot_dendrogram(x, mode = igraph_opt("dend.plot.type"), ...)
## S3 method for class 'communities'
plot_dendrogram(
x,
mode = igraph_opt("dend.plot.type"),
...,
use.modularity = FALSE,
palette = categorical_pal(8)
)x |
An object containing the community structure of a graph. See
|
mode |
Which dendrogram plotting function to use. See details below. |
... |
Additional arguments to supply to the dendrogram plotting function. |
use.modularity |
Logical scalar, whether to use the modularity values to define the height of the branches. |
palette |
The color palette to use for colored plots. |
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 = palette(),
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 = palette(),
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 rectangles 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
karate <- make_graph("Zachary")
fc <- cluster_fast_greedy(karate)
plot_dendrogram(fc)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.