| 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 = TRUE: whether to show the haplotype labels.
labels.cex = 1: size of the haplotype labels.
labels.font = 2: font of the haplotype labels.
labels.color = "black": colour of the haplotype labels.
link.color = "black": colour of the links.
link.type = 1: type of line for the links.
link.type.alt = 2: type of lines for the alternative links.
link.width = 1: line width for the links.
link.width.alt = 1: line 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 = 1: size of the mutation annotations.
mutations.font = 1: font of the mutation annotations.
mutations.frame.background = "#0000FF4D": background colour (transparent blue).
mutations.frame.border = "black": colour of the frame.
mutations.text.color = 1: colour of the mutation annotations.
mutations.arrow.color = "black": colour of the arrow pointing to the link.
mutations.arrow.type = "triangle": type of the previous arrow.
mutations.sequence.color = "#BFBFBF4D": colour of the sequence (transparent grey).
mutations.sequence.end = "round": possible choices:
"round","butt", or"square"(or alternatively 0, 1, or 2).mutations.sequence.length = 0.3: the length of the segment showing the sequence as fraction of the graphical window.
mutations.sequence.width = 5: thickness of this segment.
pie.outer.color = "black": colour of the circle around pie charts.
pie.inner.segments.color = "black": colour of the segments separating the shares of the pies.
pie.colors.function = rainbow: function used to define colours for the frequencies.
scale.ratio = 1: the scale ratio between links and symbol sizes.
show.mutation = 1: option used to show mutation or not (0).
Value
getHaploNetOptions returns a list of options. The other
function returns nothing.
Author(s)
Emmanuel Paradis
See Also
Examples
getHaploNetOptions()