R: HRG dendrogram plot

plot_dendrogram.igraphHRG {igraph} | R Documentation

## HRG dendrogram plot

### Description

Plot a hierarchical random graph as a dendrogram.

### Usage

    ## S3 method for class 'igraphHRG'
    plot_dendrogram(x, mode = igraph_opt("dend.plot.type"),
      ...)

### Arguments

`x` | An `igraphHRG`, a hierarchical random graph, as returned by the `fit_hrg` function.
`mode` | Which dendrogram plotting function to use. See details below.
`...` | Additional arguments to supply to the dendrogram plotting function.

### Details

`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`.

### Value

Returns whatever the return value was from the plotting function, `plot.phylo`, `plot.dendrogram` or `plot.hclust`.

### Author(s)

Gabor Csardi csardi.gabor@gmail.com

### Examples

    g <- make_full_graph(5) + make_full_graph(5)
    hrg <- fit_hrg(g)
    plot_dendrogram(hrg)

[Package igraph version 1.2.2 Index]