Package 'colorBlindness'

Title: Safe Color Set for Color Blindness
Description: Provide the safe color set for color blindness, the simulator of protanopia, deuteranopia. The color sets are collected from: Wong, B. (2011) <doi:10.1038/nmeth.1618>, and <http://mkweb.bcgsc.ca/biovis2012/>. The simulations of the appearance of the colors to color-deficient viewers were based on algorithms in Vienot, F., Brettel, H. and Mollon, J.D. (1999) <doi:10.1002/(SICI)1520-6378(199908)24:4%3C243::AID-COL5%3E3.0.CO;2-3>. The cvdPlot() function to generate 'ggplot' grobs of simulations were modified from <https://github.com/clauswilke/colorblindr>.
Authors: Jianhong Ou [aut, cre]
Maintainer: Jianhong Ou <[email protected]>
License: GPL (>= 2)
Version: 0.1.9
Built: 2024-11-02 03:57:16 UTC
Source: https://github.com/cran/colorBlindness

Help Index

available colors

Description

export available colors

Usage

availableColors()

Value

a character vector contain safe colors.

Examples

availableColors()

Available color palette

Description

List all the available color palettes.

Usage

availablePalette()

Value

a character vector contain available color palettes.

Examples

availablePalette()

safe colors

Description

color blindness safe colors

Usage

BLACK

ORANGE

SKY_BLUE

BLUISH_GREEN

YELLOW

BLUE

VERMILLION

REDDISH_PURPLE

safeColors

Format

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 1.

An object of class character of length 8.

References

Wong, B. (2011) <doi:10.1038/nmeth.1642> Wong, B. (2011) <doi:10.1038/nmeth.1618>

Examples

safeColors

available color variable

Description

export available color names

Usage

colorNames()

Value

a character vector contain safe colors.

Examples

colorNames()

Show color-deficiency simulations of a plot

Description

Plot the color-deficiency simulations for ggplot grob.

Usage

cvdPlot(
  plot = last_plot(),
  layout = c("origin", "deuteranope", "protanope", "desaturate")
)

Arguments

plot

The grob to be plotted.
layout

The sub-figure types. the choices are origin, deuteranope, protanope, desaturate, and enhanced, enhanced.deuteranope, enhanced.protanope, enhanced.desaturate.

Details

This function is modified from <https://github.com/clauswilke/colorblindr>

Value

An object of ggplot.

Examples

cvdPlot(displayColors(safeColors))
cvdPlot(displayColors(paletteMartin))

simulate color vision deficiency

Description

Transformation of R colors by simulating color vision deficiencies.

Usage

cvdSimulator(col, type = "deuteranope")

Arguments

col

character. A vector of colors.
type

Deficiency type, "protanope" or "deuteranope"

Details

Here use Vienot's methods but not Gustavo's methods (implemented in colorspace::simulate_cvd).

Value

colors.

References

Vienot, F., Brettel, H. and Mollon, J.D. (1999) <doi:10.1002/(SICI)1520-6378(199908)24:4 Sharma, G., Wu, W. and Dalal, E.N. (2005) <doi:10.1002/col.20070>

Examples

cvdSimulator(safeColors)

Display available palette

Description

Display all the available color palettes.

Usage

displayAvailablePalette(...)

Arguments

...

parameters could be used by geom_tile.

Value

an ggplot object

Examples

displayAvailablePalette()

display colors

Description

Display the given colors

Usage

displayColors(col, ...)

displayAllColors(col, types = c("deuteranope", "protanope", "desaturate"), ...)

Arguments

col

color set to display
...

parameters could be used by geom_tile.
types

the type of color vision deficiency.

Value

an ggplot object

Examples

displayColors(safeColors)
displayColors(paletteMartin)
displayAllColors(safeColors, color="white")
displayAllColors(paletteMartin, color="white")

convert plot to grob

Description

use grid.grabExpr or plot_to_gtable to convert plot to grob

Usage

grobify(plot)

Arguments

plot

plots

Value

grob object.

Palette for color blindness

Description

The palette could be used for heatmap or pie graph

Usage

paletteMartin

Green2Magenta16Steps

Blue2DarkRed12Steps

Blue2DarkRed18Steps

Blue2OrangeRed14Steps

Blue2DarkOrange12Steps

Blue2DarkOrange18Steps

Blue2Green14Steps

Brown2Blue10Steps

Brown2Blue12Steps

Blue2Gray8Steps

Blue2Orange8Steps

Blue2Orange10Steps

Blue2Orange12Steps

ModifiedSpectralScheme11Steps

LightBlue2DarkBlue7Steps

LightBlue2DarkBlue10Steps

PairedColor12Steps

SteppedSequential5Steps

Format

An object of class character of length 15.

An object of class character of length 16.

An object of class character of length 12.

An object of class character of length 18.

An object of class character of length 14.

An object of class character of length 12.

An object of class character of length 18.

An object of class character of length 14.

An object of class character of length 10.

An object of class character of length 12.

An object of class character of length 8.

An object of class character of length 8.

An object of class character of length 10.

An object of class character of length 12.

An object of class character of length 11.

An object of class character of length 7.

An object of class character of length 10.

An object of class character of length 12.

An object of class character of length 25.

Details

The names of the palette is approximal color name.

Green2Magenta16Steps: Useful for generic diverging data.

Blue2DarkRed12/18Steps: Useful for temperature-like data, with a subjective interpretation (blue=cold, red=hot) Blue2OrangeRed14Steps: Useful as an alternative to the red/blue temperature scale.

Blue2DarkOrange12/18Steps: Useful for data without a specific subjective color association.

Blue2Green14Steps: Useful for data with a winter (blue) vs. summer (green) association.

Brown2Blue10/12Steps: Useful for data with a dry (brown) vs. wet (blue) association.

Blue2Gray8Steps: Useful in particular for diverging data like cloudiness anomalies.

Blue2Orange8/10/12Steps: Useful for data like sea-level pressure, with ansubjective association (blue=low, wet, orange=high, dry)

ModifiedSpectralScheme11Steps: An alternative to the spectral scheme (no green)

LightBlue2DarkBlue7/10Steps: Useful for precipitation-like data.

PairedColor12Steps: Attempt at a categorical color scale with colors that may be distinguishable to all viewers

SteppedSequential5Steps: Useful for portraying levels-within-categories

Source

<http://mkweb.bcgsc.ca/biovis2012/>

References

Light A, Bartlein PJ (2004). "The End of the Rainbow? Color Schemes for Improved Data Graphics." EOS Transactions of the American Geophysical Union, 85(40), 385.

Examples

paletteMartin
Green2Magenta16Steps
Blue2DarkRed12Steps
Blue2DarkRed18Steps
Blue2OrangeRed14Steps
Blue2DarkOrange12Steps
Blue2DarkOrange18Steps
Blue2Green14Steps
Brown2Blue10Steps
Brown2Blue12Steps
Blue2Gray8Steps
Blue2Orange8Steps
Blue2Orange10Steps
Blue2Orange12Steps
ModifiedSpectralScheme11Steps
LightBlue2DarkBlue7Steps
LightBlue2DarkBlue10Steps
PairedColor12Steps
SteppedSequential5Steps

replace the colors for plots

Description

replace the colors of plots to meet the requirment of publication. Replacing red with magenta or green with turquoise. Replacing all the colored symbols in the legend.

Usage

replacePlotColor(plot)

Arguments

plot

The grob to be plotted.

Value

an object of gtable.

Examples

replacePlotColor(displayColors(c("Red", "Green", "blue")))

Auxiliary funciton to set width of pdf for journals

Description

Set the pdf width and height for journals.

Pre-sets of width for figures.

Usage

setPDFopt(
  width = c("1col", "1.5col", "0.5col", "2col"),
  presets = PRESETS$science
)

PRESETS

Arguments

width

columns.
presets

The pre-setting of width,height,family,font for pdf. Available choices: 0.5col, 1col, 1.5col, 2col.

Format

An object of class list of length 4.

Details

The family will be Helvetica. The font will be 8. The width and height will be same.

science: 0.5col=1.78 inches (4.52 cm.); 1col=3.54 inches (9 cm.); 1.5col=5 inches (12.7 cm.); 2col=7.25 inches (18.4 cm.). nature: 0.5col=2.28 inches (5.8 cm.); 1col=3.39 inches (8.6 cm.); 1.5col=4.76 inches (12.1 cm.); 2col=7 inches (17.8 cm.). cell: 0.5col=1.78 inches (4.52 cm.); 1col=3.35 inches (8.5 cm.); 1.5col=4.49 inches (11.4 cm.); 2col=6.85 inches (17.4 cm.). CA: A Cancer Journal for Clinicians 0.5col=1.62 inches (4.1 cm.); 1col=3.25 inches (8.25 cm.); 1.5col=3.87 inches (9.8 cm.); 2col=6.75 inches (17.1 cm.).

Value

A named list of all the defaults. If any arguments are supplied the return values are the old values and the result has the visibility flag turned off.

References

<http://www.sciencemag.org/sites/default/files/Figure_prep_guide.pdf>

<https://images.nature.com/full/nature-assets/aj/artworkguidelines.pdf>

Examples

op <- setPDFopt("1col")