dartR.base (version 1.0.5)

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

Description

This function draws upon a number of specified color libraries to extract a vector of colors for plotting. For use where the function 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,
  plot.display = TRUE,
  verbose = NULL
)

Value

A vector with the required number of colors

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, one of 'brewer' 'gr.palette', 'r.hcl' or 'baseR' [default scales::hue_pl].

palette

Name of the color palette to be pulled from the specified library, refer function help [default is library specific].

ncolors

number of colors to be displayed and returned [default 9 or nPop(gl)].

select

select bu number the colors to retain in the output vector; can repeat colors. [default NULL].

plot.display

if TRUE, plot the colours in the plot window [default=TRUE]

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].

Author

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

Details

Colors are chosen by specifying a library (one of 'brewer' 'gr.palette', 'r.hcl' or 'baseR') and a palette within that library. Each library has its own array of palettes, which can be listed as outlined below. Alternatively, if you specify an incorrect palette, the list of available palettes for the specified library will be listed.

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 library is not specified, then the default library 'scales' is set and the default palette of 'hue_pal is set.

If the library is set but the palette is not specified, all palettes for that library will be listed and 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 or nPop(gl) if a genlight object is specified),and the vector of colors returned by assignment 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.

See Also

gl.select.shapes

Other graphics: gl.colors(), gl.map.interactive(), gl.plot.heatmap(), gl.report.ld.map(), gl.select.shapes(), gl.smearplot(), gl.tree.nj()

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))