options_themes_haploNet: Options to Plot haploNet Objects

In pegas: Population and Evolutionary Genetics Analysis System

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()

pegas documentation built on March 7, 2023, 7:21 p.m.