Description

These functions change the graphical options to plot haplotype networks.

Usage

Arguments

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