gl.select.colors: Selects colors from one of several palettes and output as a...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Selects colors from one of several palettes and output as a vector

Description

This script draws upon a number of specified color libraries to extract a vector of colors for plotting, where the script that follows has a color parameter expecting a vector of colors.

Usage

gl.select.colors(
  x = NULL,
  library = NULL,
  palette = NULL,
  ncolors = NULL,
  select = NULL,
  verbose = NULL
)

Arguments

x	Optionally, provide a gl object from which to determine the number of populations [default NULL].
library	Name of the color library to be used [default scales::hue_pl].
palette	Name of the color palette to be pulled from the specified library [default is library specific] .
ncolors	number of colors to be displayed and returned [default 9].
select	select the colors to retain in the output vector [default NULL].
verbose	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

The available color libraries and their palettes include:

• library 'brewer' and the palettes available can be listed by RColorBrewer::display.brewer.all() and RColorBrewer::brewer.pal.info.

• library 'gr.palette' and the palettes available can be listed by grDevices::palette.pals()

• library 'r.hcl' and the palettes available can be listed by grDevices::hcl.pals()

• library 'baseR' and the palettes available are: 'rainbow','heat', 'topo.colors','terrain.colors','cm.colors'.

If the nominated palette is not specified, all the palettes will be listed a nd a default palette will then be chosen.

The color palette will be displayed in the graphics window for the requested number of colors (or 9 if not specified),and the vector of colors returned for later use.

The select parameter can be used to select colors from the specified ncolors. For example, select=c(1,1,3) will select color 1, 1 again and 3 to retain in the final vector. This can be useful for fine-tuning color selection, and matching colors and shapes.

Value

A vector with the required number of colors

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.select.shapes

Other Exploration/visualisation functions: gl.pcoa.plot(), gl.select.shapes(), gl.smearplot()

Examples

# SET UP DATASET
gl <- testset.gl
levels(pop(gl))<-c(rep('Coast',5),rep('Cooper',3),rep('Coast',5),
rep('MDB',8),rep('Coast',7),'Em.subglobosa','Em.victoriae')
# EXAMPLES -- SIMPLE
colors <- gl.select.colors()
colors <- gl.select.colors(library='brewer',palette='Spectral',ncolors=6)
colors <- gl.select.colors(library='baseR',palette='terrain.colors',ncolors=6)
colors <- gl.select.colors(library='baseR',palette='rainbow',ncolors=12)
colors <- gl.select.colors(library='gr.hcl',palette='RdBu',ncolors=12)
colors <- gl.select.colors(library='gr.palette',palette='Pastel 1',ncolors=6)
# EXAMPLES -- SELECTING colorS
colors <- gl.select.colors(library='baseR',palette='rainbow',ncolors=12,select=c(1,1,1,5,8))
# EXAMPLES -- CROSS-CHECKING WITH A GENLIGHT OBJECT
colors <- gl.select.colors(x=gl,library='baseR',palette='rainbow',ncolors=12,select=c(1,1,1,5,8))

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.