R: Options to Plot haploNet Objects

getHaploNetOptions {pegas} | R Documentation

## Options to Plot haploNet Objects

### Description

These functions change the graphical options to plot haplotype networks.

### Usage

    getHaploNetOptions()
    setHaploNetOptions(...)

### Arguments

`...` | option(s) and value(s) to be changed (separated by commas if several).

### Details

The options are listed below with their default values. Most of these values use the standard R graphical paramters (see `par`).

- bg = "transparent"the background colour of the plot.

- labels = TRUEwhether to show the haplotype labels.

- labels.cex = 1size of the haplotype labels.

- labels.font = 2font of the haplotype labels.

- link.color = "black"colour of the links.

- link.type = 1type of line for the links.

- link.type.alt = 2type of lines for the alternative links.

- link.width = 1line width for the links.

- link.width.alt = 1line width for the alternative links.

- haplotype.inner.color = "white"colour used inside the haplotype symbols.

- haplotype.outer.color = "black"colour used for the border of the haplotype symbols.

- mutations.cex = 1size of the mutation annotations.

- mutations.font = 1font of the mutation annotations.

- mutations.frame.background = "#0000FF4D"transparent blue.

- mutations.frame.border = "black"

- mutations.text.color = 1colour of the mutation annotations.

- mutations.arrow.color = "black"colour of the arrow pointing to the link.

- mutations.arrow.type = "triangle"type of the above arrow.

- mutations.sequence.color = "#BFBFBF4D"transparent grey.

- mutations.sequence.end = "round"possible choices: `"round"`, `"butt"`, or `"square"` (or alternatively 0, 1, or 2).

- mutations.sequence.length = 0.3the length of the segment showing the sequence as fraction of the graphical window.

- mutations.sequence.width = 5thickness of this segment.

- pie.outer.color = "black"

- pie.inner.segments.color = "black"

- pie.colors.function = rainbowfunctio used to define colours for the frequencies.

- scale.ratio = 1

- show.mutation = 1

### Value

`getHaploNetOptions` returns a list of options. The other function returns nothing.

### Author(s)

Emmanuel Paradis

### See Also

`plot.haploNet`, `mutations`

### Examples

    getHaploNetOptions()

[Package pegas version 1.1 Index]