using color in r

7/31/2019 Using Color in R

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St ower s I nst it ut e f or Medical Resear chR/ Bioconduct or Discussion Gr oup

Ear l F. GlynnScient if ic Pr ogr ammer

17 July 2007

Using Color in R


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Using Color in R Color Basics in R

Color Spaces

Color Gr adient s / Color Ramps

Color Blindness

Why Dont Screen Colors Mat ch Pr int out ?

Color s Tips


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Using Color in R

Color Basics: Palet t e> barplot(rep(1,8), yaxt="n", col=1:8)

> palette()

[1] "black" "red" "green3" "blue" "cyan"

[6] "magenta" "yellow" "gray"


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Using Color in R

Color Basics: Palet t e> barplot(rep(1,8), yaxt="n", col=1:8)

> barplot(rep(1,8), yaxt="n", col=palette())

> barplot(rep(1,8), yaxt="n",

col=c("black", "red", "green3", "blue","cyan", "magenta", "yellow", "gray"))

Integer color numbers represent offsets into the palette table


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Using Color in R

Color Basics: Palet t e> palette(rainbow(10)) # Redefine palette

> palette()

[1] "red" "#FF9900" "#CCFF00" "#33FF00" "#00FF66"

[6] "cyan" "#0066FF" "#3300FF" "#CC00FF" "#FF0099"

> # colors are "recycled" if necessary

> barplot(rep(1,20),col=1:20, yaxt="n")

> palette("default")

> palette()

[1] "black" "red" "green3"

"blue" "cyan"


RGB Hex Constants

Color Names

Specify number of colors withrainbow

Recycled Colors

Cut/Paste

Bitmap


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> 0:8 / 8

[1] 0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000

> palette(gray(0:8 / 8))

> palette()

[1] "black" "#202020" "gray25" "#606060" "#808080"

[6] "#9F9F9F" "gray75" "#DFDFDF" "white"

> # colors are "recycled" if necessary

> barplot(rep(1,20),col=1:20, yaxt="n")

>

> palette("default")

> palette()

[1] "black" "red" "green3"

"blue" "cyan"


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Using Color in R

Color Basics: Palet t e

RGB Hex Constants

Recycled Colors

Specify vector of floats 0.0 to 1.0 withgrey/gray


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> colors() # or colours()

[1] "white" "aliceblue" "antiquewhite"

[4] "antiquewhite1" "antiquewhite2" "antiquewhite3"

[655] "yellow3" "yellow4" "yellowgreen"

> colors()[grep("red", colors())][1] "darkred" "indianred" "indianred1"

[4] "indianred2" "indianred3" "indianred4"

[7] "mediumvioletred" "orangered" "orangered1"

[10] "orangered2" "orangered3" "orangered4"

[13] "palevioletred" "palevioletred1" "palevioletred2"

[16] "palevioletred3" "palevioletred4" "red"

[19] "red1" "red2" "red3"

[22] "red4" "violetred" "violetred1"[25] "violetred2" "violetred3" "violetred4"

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Using Color in R

Color Basics: Color Names

Color names from C:\Program Files\R\R-2.5.1\etc\rgb.txt


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Using Color in R


http://research.stowers-institute.org/efg/R/Color/Chart/index.htm


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Using Color in R


Print seven page table to compare screen colors with printed colors.

http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf

Alphabet icalexcept f ir stcolor , which iswhit e


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Using Color in R

Color Basics: Hex Const ant s

Numbers represented in "base 16" are called "hexadecimal".

Hex "FF" is largest value represented by one byte (8 bits).

Hex Decimal

0 0

1 1

2 2

3 34 4

5 5

6 6

7 7

8 8

9 9

A 10

B 11C 12

D 13

E 14

F 15

Index Color Name #rrggbb red green blue

Hex "FF" = 15*161 + 15*160 = 255

Hex "00" to "FF" can be interpreted as 0.0 to 1.0.

"Sat ur at ed"Pr imar y Color s

"Unsat ur at ed"shades of gray


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Using Color in R

Color BasicsI n R Color can be repr esent ed by

index int o palet t e

color name

hex const ant (24-bit "Tr ue Color ":

2563

color s = 16,777,216 color s)


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Using Color in R

Color BasicsI n R many obj ect s can t ake on dif f er ent color s:

point s

l ines

axes

t ext

legends

backgr ound


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> palette()[1] "black" "red" "green3" "blue" "cyan"


> x y plot(x,y, col=1:5,

pch=CIRCLE plot(x,y,

col=c("black", "red", "green3", "blue", "cyan"),pch=CIRCLE, cex=2)

> plot(x,y,

col=c("#000000", "#FF0000", "green3", 4, 5),

pch=CIRCLE, cex=2)

Hex #rrggbb Color name Palette Index

Using Color in R

Color Basics: Point s

-2 -1 0 1 2

0

1

2

3

4

x

y


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Using Color in R

Color Basics: Point sn


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> plot(log2(somite$Signal.1L), log2(somite$Signal.1R))

How to associate color with p-values at each point?

p=1p=0

> library(gplots)

> palette(rev(rich.colors(32)))

Colors 1 to 32

Using Color in R



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> palette( rev(rich.colors(32)) ) # colors: 1 to 32

> plot(log2(somite$Signal.1L), log2(somite$Signal.1R),

col=1 + 31*somite$worst.p) # col values from 1 to 32

p=1p=0

Using Color in R



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Using Color in R

Color Basics: Point s and Lines

-50 0 50 100 150 200 250 300

-50

0

50

100

150

200

250

300

-500

50100

150200 250

300

red

green

blue

Red-Green-Blue 3D Plot ofcolors()

library(scatterplot3d)

?scatterplot3d

# Example 6


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Using Color in R

Color Basics: Axes and TextBOTTOM


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Using Color in R

Color Basics: LegendsTime


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Using Color in R

Color Basics: Backgr ound

par(bg="light blue")

x


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Color Spaces


Color Blindness


Color s Tips


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Using Color in R

Color Space: RGB Color Model

Color is additive in the RGB Color Model.Coordinate values not always obvious.

#rrggbb R G B

> rgb(1,0,0)

[1] "#FF0000"

> rgb(0,1,0)

[1] "#00FF00"

> rgb(1,1,0)

[1] "#FFFF00"

> rgb(255,0,0, maxColorValue=255)

[1] "#FF0000"

> col2rgb(c("blue", "yellow"))

[,1] [,2]

red 0 255green 0 255

blue 255 0


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Using Color in R

Red-Gr een-Blue Color Cube

Red

Green

Blue

Yellow

Magenta

Cyan

Black

White

Grey Line

255

0, 0, 0

255, 255, 255

255

255

B = 0 to 255G = 0 to 255R = 0 to 255

0.0 to 1.0

0 to 255 (8-bits)

24-bit graphics:

256 x 256 x 256 = 16,777,216 colors

256 shades of grey

Not all colors

are perceivable

on all devices

Cont rast ing Colors?


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Using Color in R

Color Space: HSV

Source: http://scien.stanford.edu/class/psych221/projects/02/sojeong/

Hue-Sat ur at ion-ValueMat ch percept ion of color bet t er t han RGB


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Using Color in R

Color Space: HSVHue-Sat ur at ion-Value

> hsv(1,1,1)

[1] "#FF0000"

> hsv(1/3,1,1)

[1] "#00FF00"

> hsv(2/3,1,1)

[1] "#0000FF"

hue rgb2hsv(col2rgb("blue"))

[,1]

h 0.6666667

s 1.0000000

v 1.0000000

0.000

0.025

0.050

0.075

0.100

0.125

0.150

0.1750.200

0.2250.2500.275

0.300

0.325

0.350

0.375

0.400

0.425

0.450

0.475

0.500

0.525

0.550

0.575

0.600

0.625

0.650

0.6750.700

0.725 0 .7 500.775

0.800

0.825

0.850

0.875

0.900

0.925

0.950

0.975

HSV (S=1, V=1)

Cont r ast ing Colors?


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Using Color in R

Color Spaceshelp(package=color space)


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Color Spaces


Color Blindness


Color s Tips


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Using Color in R


rainbow

heat.colors

terrain.colors

topo.colors

cm.colors (cyan-magenta)

gray

par(mfrow=c(6,1), mar=c(3,1,0,1))

BOTTOM


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Using Color in R

Color Gr adient s / Color Rampscolor Ramp and colorRampPalet t e added in R 2.1.0

m


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Using Color in R

Color Gr adient s / Color RampsHCL (Hue, Chr oma, Luminance)

> ?hcl

> barplot(rep(1, 20), col = hcl(seq(0, 360, length = 20)))

0.0

0.4

0.8

See: HCL(Hue-Chr oma-Luminance)-based Color Palet t es in R

ht t p:/ / cran.r -proj ect .or g/ doc/ vignet t es/ vcd/ hcl-color s.pdf


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Using Color in R


> library(RColorBrewer)

> display.brewer.all()

RColorBr ewer Package

BrBGPiYG

PRGnPuOrRdBuRdGy

RdYlBuRdYlGn

Spectral

AccentDark2PairedPastel1

Pastel2Set1Set2Set3

BluesBuGnBuPuGnBu

GreensGreys

OrangesOrRdPuBu

PuBuGnPuRd

PurplesRdPuRedsYlGnYlGnBu

YlOrBrYlOrRd


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Using Color in R

Color Gr adient s / Color RampsRepr esent at ive Color f or Given Wavelengt h

Sour ce: ht t p:/ / www.ef g2.com/ Lab/ ScienceAndEngineer ing/ Spect r a.ht m


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Color Spaces


Color Blindness


Color s Tips


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Using Color in R

Color Blindness

Nor mal Color Vision: 25, 29, 45, 56, 6, 8Red-Gr een Color Blind: 25, spot s, spot s, 56, spot s, spot s

I shihar a Test f or Color Blindness

Sour ce: ht t p:/ / www.toledo-bend.com/ colorblind/ I shihar a.ht ml

About 1 in 12 have some sort of color deficiency:About ~8% of men and ~0.4% of women in the US.

ht t p:/ / en.wikipedia.or g/ wiki/ Color_blindness


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Using Color in R

Color BlindnessR dichromat Package: Color Schemes f or dichromat s

library(dichromat)

par(mfcol=c(1,2))

N


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Using Color in R


library(dichromat)

par(mar=c(1,2,1,1))

layout(matrix(1:6,ncol=1))

image(1:10,1,matrix(1:10, ncol=1),

col=colorschemes$BrowntoBlue.10,

main="Brown to Blue (10)", axes=FALSE)

image(1:100,1,matrix(1:100 ,ncol=1),

col=colorRampPalette(colorschemes$BrowntoBlue.10,space="Lab")(100),

main="Brown to Blue Ramp", axes=FALSE)


col=dichromat(colorschemes$BrowntoBlue.10),

main="Brown to Blue (10) -- deuteranopia", axes=FALSE)

image(1:12,1,matrix(1:12, ncol=1),col=colorschemes$Categorical.12,

main="Categorical (12)", axes=FALSE)


col=dichromat(colorschemes$Categorical.12),

main="Categorical (12) -- deuteranopia", axes=FALSE)

image(1:12,1,matrix(1:12,ncol=1),

col=dichromat(colorschemes$Categorical.12, "protan"),

main="Categorical (12) -- protanopia", axes=FALSE)


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Using Color in R


Brown to Blue (10)

Brown to Blue Ramp

Brown to Blue (10) -- deuteranopia

Categorical (12)

Categorical (12) -- deuteranopia

Categorical (12) -- protanopia


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Color Spaces


Color Blindness


Color s Tips


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Using Color in R


Concept ualDiagram ofAl l Colors(2D Slice)


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Using Color in R


Each DeviceHas OwnGamut ofColors


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From Visualization of Expanded Printing Gamuts Using 3-Dimensional Convex Hullsby Karl Guyler, Hallmark Cards, Kansas City

Color calibr at ion can be used t o minimize needless dif f erences

Using Color in R

3D Color Gamut


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Using Color in R


Dif f er ent color gamut s bet ween devices:How should a color be repr esent ed if it doesn' t exist

on a device?

I mper f ect conver sions:CRT screens wit h RGB (Red-Gr een-Blue) addit ive

colors must be conver t ed t o CMYK

(Cyan-Magent a-Yellow-Black) subt r act ive colors

Color f idelit y may not be accur at e

Paper / ink dif f er ences


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Color Spaces


Color Blindness


Color s Tips


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Using Color in R

Color Tips Avoid unnecessar y use of color .

Use br ight color s wit h smallgr aphics t o make t hem st and out .

Be consist ent in use of color .

Don' t use color as only at t r ibut et o show dif f er ence. E.g., considercolor and line t ype.

Also see: Cool Color Comment ar y, ht t p:/ / www.public-speaking.or g/ public-speaking-color- ar t icle.htm


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Using Color in R

Color Tips: Palet t esQualit at ive Palet t e:

all same per cept ual weight / impor t ance

t ypical applicat ion: bar plot

Sequent ial Palet t e

f or coding numer ical inf or mat ion in a r ange

t ypical applicat ion: heat map

Diver ging Palet t e

Like Sequent ial Palet t e but wit h neut r al value

Sour ce: Choosing Color Palet t es f or St at ist ical Gr aphicsht t p:/ / epub.wu-wien.ac.at / dyn/ vir lib/ wp/ mediat e/ epub-wu-01_abd.pdf ?I D=epub-wu-01_abd


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Using Color in R

Ref er encesColour for Presentation Graphicshttp://www.stat.auckland.ac.nz/~ihaka/colour/color-talk.pdf

Why should Engineers and Scientists be worried about color?http://www.research.ibm.com/people/l/lloydt/color/color.HTM

using color in r

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