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Introduction

Safe colorsets

Color vision deficiency (CVD) simulator

How to use this package

Collection of safe colors

replacePlotColor effect for Ishihara Color Test.

Session Info

References

colorBlindness Guide
Jianhong Ou
2021-04-16

Introduction
Color blindness is color vision deficiency, which means people with color blindness may be not aware of
differences among colors that are obvious to the people without it. This package is designed to provide a
collection of safe colors for plots such as heatmaps, pie chart, and try to find a solution for acceptable
figures for all the end users.

Safe colorsets
There are lots of packages already collected lots of safe colors. I list some of them, but not limited here.

munsell (https://CRAN.R-project.org/package=munsell)

viridis (https://CRAN.R-project.org/package=viridis) and RColorBrewer (https://CRAN.R-

project.org/package=RColorBrewer)

dichromat (https://CRAN.R-project.org/package=dichromat)

colorblindr (https://github.com/clauswilke/colorblindr)

shades (https://CRAN.R-project.org/package=shades)

ggsci (https://CRAN.R-project.org/package=ggsci)

For this package, I will try to collect as much as possible safe color sets ready to use.

Color vision deficiency (CVD) simulator

The tool used to simulate the color vision deficiency is called CVD simulator. I list some of packages here
with CVD simulator.

Hans Brettel 1997(Brettel et al., 1997)

Francoise Vienot 1999(Viénot et al., 1999) (implemented in this package and package dichromat
(https://CRAN.R-project.org/package=dichromat) )

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Gustavo M. Machado 2009(Machado et al., 2009) (implemented in package colorspace

(https://CRAN.R-project.org/package=colorspace))

Claire D. McWhite and Claus O. Wilke. colorblindr (https://github.com/clauswilke/colorblindr)

How to use this package

Use safe color to plot
To plot figures by colors of this package, there are three steps:

1. select correct safe color set.

2. plot with the color set.

3. check the plot by CVD simulator.

For example if we want to plot a heatmap.

library(colorBlindness)
mat <- matrix(1:81, nrow = 9, ncol = 9)

library(ggplot2)
library(reshape2)
mat1 <- melt(t(mat[9:1, ]))
len <- length(Blue2DarkRed12Steps)-1
mat1$v2 <- cut(mat1$value,
breaks = seq(0,ceiling(81/len)*len,
length.out = len+1))
ht <- ggplot(mat1) +
geom_tile(aes(x=Var1, y=Var2, fill=v2)) +
scale_fill_manual(values=Blue2DarkRed12Steps) +
theme_bw()
# check the plot by CVD simulator
cvdPlot(ht)

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replace the color of a plot to safe color

If you have figures which is not safe to color blindness people, you can try to replace the colors by
replacePlotColor function.

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

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If you have a fluorescence image and want to change the colors, you can read the figure and view the effect
of color changed figure. If it is acceptable, you can draw it into a file.

library(grid)
library(png)
path <- system.file("extdata", package = "colorBlindness")
img <- readPNG(file.path(path, "fluorescence.microscopy.images.png"))
g <- rasterGrob(img, interpolate=TRUE)
grid.draw(cvdPlot(g,
layout = c("origin", "deuteranope", "protanope",
"enhanced", "enhanced.deuteranope",
"enhanced.protanope")))

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newImg <- replacePlotColor(g)

outfile <- tempfile(fileext = ".png")
png(outfile)
grid.draw(newImg)
dev.off()

## quartz_off_screen
## 2

Best approach to make figures

To plot figures for literature, there serveral things we need to consider:

1. Figure format and size;

2. Font family and size;

3. Proper figure colors that are distinguishable by people with colorblindness and for printed in black
and white.

setPDFopt function can provide you preset figure size for PDF outputs.

pdf.options()[c("width", "height", "pointsize")]

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## $width
## [1] 7
##
## $height
## [1] 7
##
## $pointsize
## [1] 12

setPDFopt()
pdf.options()[c("width", "height", "pointsize")]

## $width
## 1col
## 3.54
##
## $height
## 1col
## 3.54
##
## $pointsize
## [1] 8

Collection of safe colors

There are more than 15 Color palettes for color blindness from Martin Krzywinski and et al.

See also GETTING INTO VISUALIZATION OF LARGE BIOLOGICAL DATA SETS

(http://mkweb.bcgsc.ca/biovis2012/krzywinski-visualizing-biological-data.pdf) and “Controversial Color Use
on Maps”(Brewer, 1997).

displayAvailablePalette(color="white")

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The displayAllColors funciton can be used to show the effect for color vision deficiency. Here we dispaly
color collection from Bang Wong(Wong, 2011).

displayAllColors(safeColors, color="white")

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replacePlotColor effect for Ishihara

Color Test.
## replace the color of a file

ishihara29 <- system.file("extdata", "Plate3.png", package = "colorBlindness")

library(png)
img <- readPNG(ishihara29)
g <- rasterGrob(img, interpolate=TRUE)
grid.draw(cvdPlot(g,
layout = c("origin", "deuteranope", "protanope",
"enhanced", "enhanced.deuteranope",
"enhanced.protanope")))

Session Info
sessionInfo()

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## R version 4.0.5 (2021-03-31)

## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] png_0.1-7 reshape2_1.4.4 ggplot2_3.3.3
## [4] colorBlindness_0.1.9
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 highr_0.8 plyr_1.8.6 bslib_0.2.4
## [5] compiler_4.0.5 pillar_1.6.0 jquerylib_0.1.3 tools_4.0.5
## [9] digest_0.6.27 jsonlite_1.7.2 evaluate_0.14 lifecycle_1.0.0
## [13] tibble_3.1.0 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.10
## [17] DBI_1.1.1 yaml_2.2.1 xfun_0.22 withr_2.4.1
## [21] stringr_1.4.0 dplyr_1.0.5 knitr_1.32 gridGraphics_0.5-1
## [25] generics_0.1.0 sass_0.3.1 vctrs_0.3.7 cowplot_1.1.1
## [29] tidyselect_1.1.0 glue_1.4.2 R6_2.5.0 fansi_0.4.2
## [33] rmarkdown_2.7 farver_2.1.0 purrr_0.3.4 magrittr_2.0.1
## [37] scales_1.1.1 htmltools_0.5.1.1 ellipsis_0.3.1 assertthat_0.2.1
## [41] colorspace_2.0-0 labeling_0.4.2 utf8_1.2.1 stringi_1.5.3
## [45] munsell_0.5.0 crayon_1.4.1

References
Brettel, H., Viénot, F., & Mollon, J. D. (1997). Computerized simulation of color appearance for dichromats.
JOSA A, 14(10), 2647–2655.

Brewer, C. A. (1997). Spectral schemes: Controversial color use on maps. Cartography and Geographic
Information Systems, 24(4), 203–220. https://doi.org/10.1559/152304097782439231
(https://doi.org/10.1559/152304097782439231)

Machado, G. M., Oliveira, M. M., & Fernandes, L. A. (2009). A physiologically-based model for simulation of
color vision deficiency. IEEE Transactions on Visualization and Computer Graphics, 15(6), 1291–1298.

Viénot, F., Brettel, H., & Mollon, J. D. (1999). Digital video colourmaps for checking the legibility of displays by
dichromats. Color Research & Application: Endorsed by Inter-Society Color Council, the Colour Group (Great
Britain), Canadian Society for Color, Color Science Association of Japan, Dutch Society for the Study of
Color, the Swedish Colour Centre Foundation, Colour Society of Australia, Centre Français de La Couleur,
24(4), 243–252.

Wong, B. (2011). Points of view: Color blindness. Nature Publishing Group.

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