diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index ebcf82f..99ce456 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index ae00b36..9ad244f 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 5d9f68e..a919316 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/articles/ggsci.html b/docs/articles/ggsci.html index c1e1d82..fd0d9e6 100644 --- a/docs/articles/ggsci.html +++ b/docs/articles/ggsci.html @@ -35,7 +35,7 @@ ggsci - 2.8.9001 + 2.9 @@ -79,7 +79,7 @@

Scientific Journal and Sci-Fi Themed
Color Palettes for ggplot2

Nan Xiao <https://nanx.me>
Miaozhu Li <http://miaozhu.li>

-

2018-05-07

+

2018-05-13

Source: vignettes/ggsci.Rmd @@ -117,112 +117,156 @@

-

NPG

-

scale_color_npg() scale_fill_npg()

-

"nrc"

-

pal_npg()

+NPG + +scale_color_npg() scale_fill_npg() + +"nrc" +pal_npg() -

AAAS

-

scale_color_aaas() scale_fill_aaas()

-

"default"

-

pal_aaas()

+AAAS + +scale_color_aaas() scale_fill_aaas() + +"default" +pal_aaas() -

NEJM

-

scale_color_nejm() scale_fill_nejm()

-

"default"

-

pal_nejm()

+NEJM + +scale_color_nejm() scale_fill_nejm() + +"default" +pal_nejm() -

Lancet

-

scale_color_lancet() scale_fill_lancet()

-

"lanonc"

-

pal_lancet()

+Lancet + +scale_color_lancet() scale_fill_lancet() + +"lanonc" +pal_lancet() -

JAMA

-

scale_color_jama() scale_fill_jama()

-

"default"

-

pal_jama()

+JAMA + +scale_color_jama() scale_fill_jama() + +"default" +pal_jama() -

JCO

-

scale_color_jco() scale_fill_jco()

-

"default"

-

pal_jco()

+JCO + +scale_color_jco() scale_fill_jco() + +"default" +pal_jco() -

UCSCGB

-

scale_color_ucscgb() scale_fill_ucscgb()

-

"default"

-

pal_ucscgb()

+UCSCGB + +scale_color_ucscgb() scale_fill_ucscgb() + +"default" +pal_ucscgb() -

D3

-

scale_color_d3()
scale_fill_d3()

-

"category10" "category20" "category20b" "category20c"

-

pal_d3()

+D3 + +scale_color_d3()
scale_fill_d3() + + +"category10" "category20" "category20b" "category20c" + +pal_d3() -

LocusZoom

-

scale_color_locuszoom() scale_fill_locuszoom()

-

"default"

-

pal_locuszoom()

+LocusZoom + +scale_color_locuszoom() scale_fill_locuszoom() + +"default" +pal_locuszoom() -

IGV

-

scale_color_igv() scale_fill_igv()

-

"default"
"alternating"

-

pal_igv()

+IGV + +scale_color_igv() scale_fill_igv() + + +"default"
"alternating" + +pal_igv() -

UChicago

-

scale_color_uchicago() scale_fill_uchicago()

-

"default"
"light"
"dark"

-

pal_uchicago()

+UChicago + +scale_color_uchicago() scale_fill_uchicago() + + +"default"
"light"
"dark" + +pal_uchicago() -

Star Trek

-

scale_color_startrek() scale_fill_startrek()

-

"uniform"

-

pal_startrek()

+Star Trek + +scale_color_startrek() scale_fill_startrek() + +"uniform" +pal_startrek() -

Tron Legacy

-

scale_color_tron() scale_fill_tron()

-

"legacy"

-

pal_tron()

+Tron Legacy + +scale_color_tron() scale_fill_tron() + +"legacy" +pal_tron() -

Futurama

-

scale_color_futurama() scale_fill_futurama()

-

"planetexpress"

-

pal_futurama()

+Futurama + +scale_color_futurama() scale_fill_futurama() + +"planetexpress" +pal_futurama() -

Rick and Morty

-

scale_color_rickandmorty() scale_fill_rickandmorty()

-

"schwifty"

-

pal_rickandmorty()

+Rick and Morty + +scale_color_rickandmorty() scale_fill_rickandmorty() + +"schwifty" +pal_rickandmorty() -

The Simpsons

-

scale_color_simpsons() scale_fill_simpsons()

-

"springfield"

-

pal_simpsons()

+The Simpsons + +scale_color_simpsons() scale_fill_simpsons() + +"springfield" +pal_simpsons() -

GSEA

-

scale_color_gsea() scale_fill_gsea()

-

"default"

-

pal_gsea()

+GSEA + +scale_color_gsea() scale_fill_gsea() + +"default" +pal_gsea() -

Material Design

-

scale_color_material() scale_fill_material()

-

"red" "pink"
"purple" "deep-purple"
"indigo" "blue"
"light-blue" "cyan"
"teal" "green"
"light-green" "lime"
"yellow" "amber"
"orange" "deep-orange"
"brown" "grey"
"blue-grey"

-

pal_material()

+Material Design + +scale_color_material() scale_fill_material() + + +"red" "pink"
"purple" "deep-purple"
"indigo" "blue"
"light-blue" "cyan"
"teal" "green"
"light-green" "lime"
"yellow" "amber"
"orange" "deep-orange"
"brown" "grey"
"blue-grey" + +pal_material() @@ -231,169 +275,169 @@

Discrete Color Palettes

We will use scatterplots with smooth curves, and bar plots to demonstrate the discrete color palettes in ggsci.

-
library("ggsci")
-library("ggplot2")
-library("gridExtra")
-
-data("diamonds")
-
-p1 = ggplot(subset(diamonds, carat >= 2.2),
-       aes(x = table, y = price, colour = cut)) +
-  geom_point(alpha = 0.7) +
-  geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
-  theme_bw()
-
-p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
-       aes(x = depth, fill = cut)) +
-  geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
-  theme_bw()
+
library("ggsci")
+library("ggplot2")
+library("gridExtra")
+
+data("diamonds")
+
+p1 = ggplot(subset(diamonds, carat >= 2.2),
+       aes(x = table, y = price, colour = cut)) +
+  geom_point(alpha = 0.7) +
+  geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) +
+  theme_bw()
+
+p2 = ggplot(subset(diamonds, carat > 2.2 & depth > 55 & depth < 70),
+       aes(x = depth, fill = cut)) +
+  geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
+  theme_bw()

NPG

The NPG palette is inspired by the plots in the journals published by Nature Publishing Group:

-
p1_npg = p1 + scale_color_npg()
-p2_npg = p2 + scale_fill_npg()
-grid.arrange(p1_npg, p2_npg, ncol = 2)
+
p1_npg = p1 + scale_color_npg()
+p2_npg = p2 + scale_fill_npg()
+grid.arrange(p1_npg, p2_npg, ncol = 2)

AAAS

The AAAS palette is inspired by the plots in the journals published by American Association for the Advancement of Science:

-
p1_aaas = p1 + scale_color_aaas()
-p2_aaas = p2 + scale_fill_aaas()
-grid.arrange(p1_aaas, p2_aaas, ncol = 2)
+
p1_aaas = p1 + scale_color_aaas()
+p2_aaas = p2 + scale_fill_aaas()
+grid.arrange(p1_aaas, p2_aaas, ncol = 2)

NEJM

The NEJM palette is inspired by the plots in The New England Journal of Medicine:

-
p1_nejm = p1 + scale_color_nejm()
-p2_nejm = p2 + scale_fill_nejm()
-grid.arrange(p1_nejm, p2_nejm, ncol = 2)
+
p1_nejm = p1 + scale_color_nejm()
+p2_nejm = p2 + scale_fill_nejm()
+grid.arrange(p1_nejm, p2_nejm, ncol = 2)

Lancet

The Lancet palette is inspired by the plots in Lancet journals, such as Lancet Oncology:

-
p1_lancet = p1 + scale_color_lancet()
-p2_lancet = p2 + scale_fill_lancet()
-grid.arrange(p1_lancet, p2_lancet, ncol = 2)
+
p1_lancet = p1 + scale_color_lancet()
+p2_lancet = p2 + scale_fill_lancet()
+grid.arrange(p1_lancet, p2_lancet, ncol = 2)

JAMA

The JAMA palette is inspired by the plots in The Journal of the American Medical Association:

-
p1_jama = p1 + scale_color_jama()
-p2_jama = p2 + scale_fill_jama()
-grid.arrange(p1_jama, p2_jama, ncol = 2)
+
p1_jama = p1 + scale_color_jama()
+p2_jama = p2 + scale_fill_jama()
+grid.arrange(p1_jama, p2_jama, ncol = 2)

JCO

The JCO palette is inspired by the the plots in Journal of Clinical Oncology:

-
p1_jco = p1 + scale_color_jco()
-p2_jco = p2 + scale_fill_jco()
-grid.arrange(p1_jco, p2_jco, ncol = 2)
+
p1_jco = p1 + scale_color_jco()
+p2_jco = p2 + scale_fill_jco()
+grid.arrange(p1_jco, p2_jco, ncol = 2)

UCSCGB

The UCSCGB palette is from the colors used by UCSC Genome Browser for representing chromosomes. This palette has been intensively used in visualizations produced by Circos.

-
p1_ucscgb = p1 + scale_color_ucscgb()
-p2_ucscgb = p2 + scale_fill_ucscgb()
-grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
+
p1_ucscgb = p1 + scale_color_ucscgb()
+p2_ucscgb = p2 + scale_fill_ucscgb()
+grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)

D3

The D3 palette is from the categorical colors used by D3.js (version 3.x and before). There are four palette types (category10, category20, category20b, category20c) available.

-
p1_d3 = p1 + scale_color_d3()
-p2_d3 = p2 + scale_fill_d3()
-grid.arrange(p1_d3, p2_d3, ncol = 2)
+
p1_d3 = p1 + scale_color_d3()
+p2_d3 = p2 + scale_fill_d3()
+grid.arrange(p1_d3, p2_d3, ncol = 2)

LocusZoom

The LocusZoom palette is based on the colors used by LocusZoom.

-
p1_locuszoom = p1 + scale_color_locuszoom()
-p2_locuszoom = p2 + scale_fill_locuszoom()
-grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
+
p1_locuszoom = p1 + scale_color_locuszoom()
+p2_locuszoom = p2 + scale_fill_locuszoom()
+grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)

IGV

The IGV palette is from the colors used by Integrative Genomics Viewer for representing chromosomes. There are two palette types (default, alternating) available.

-
p1_igv_default = p1 + scale_color_igv()
-p2_igv_default = p2 + scale_fill_igv()
-grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)
+
p1_igv_default = p1 + scale_color_igv()
+p2_igv_default = p2 + scale_fill_igv()
+grid.arrange(p1_igv_default, p2_igv_default, ncol = 2)

UChicago

-

The UChicago palette is based on the colors used by The University of Chicago. There are three palette types (default, light, dark) available.

-
p1_uchicago = p1 + scale_color_uchicago()
-p2_uchicago = p2 + scale_fill_uchicago()
-grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
+

The UChicago palette is based on the colors used by the University of Chicago. There are three palette types (default, light, dark) available.

+
p1_uchicago = p1 + scale_color_uchicago()
+p2_uchicago = p2 + scale_fill_uchicago()
+grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)

Star Trek

This palette is inspired by the (uniform) colors in Star Trek:

-
p1_startrek = p1 + scale_color_startrek()
-p2_startrek = p2 + scale_fill_startrek()
-grid.arrange(p1_startrek, p2_startrek, ncol = 2)
+
p1_startrek = p1 + scale_color_startrek()
+p2_startrek = p2 + scale_fill_startrek()
+grid.arrange(p1_startrek, p2_startrek, ncol = 2)

Tron Legacy

This palette is inspired by the colors used in Tron Legacy. It is suitable for displaying data when using a dark theme:

-
p1_tron = p1 + theme_dark() + theme(
-    panel.background = element_rect(fill = "#2D2D2D"),
-    legend.key = element_rect(fill = "#2D2D2D")) +
-  scale_color_tron()
-p2_tron = p2 + theme_dark() + theme(
-    panel.background = element_rect(fill = "#2D2D2D")) +
-  scale_fill_tron()
-grid.arrange(p1_tron, p2_tron, ncol = 2)
+
p1_tron = p1 + theme_dark() + theme(
+    panel.background = element_rect(fill = "#2D2D2D"),
+    legend.key = element_rect(fill = "#2D2D2D")) +
+  scale_color_tron()
+p2_tron = p2 + theme_dark() + theme(
+    panel.background = element_rect(fill = "#2D2D2D")) +
+  scale_fill_tron()
+grid.arrange(p1_tron, p2_tron, ncol = 2)

Futurama

This palette is inspired by the colors used in the TV show Futurama:

-
p1_futurama = p1 + scale_color_futurama()
-p2_futurama = p2 + scale_fill_futurama()
-grid.arrange(p1_futurama, p2_futurama, ncol = 2)
+
p1_futurama = p1 + scale_color_futurama()
+p2_futurama = p2 + scale_fill_futurama()
+grid.arrange(p1_futurama, p2_futurama, ncol = 2)

Rick and Morty

This palette is inspired by the colors used in the TV show Rick and Morty:

-
p1_rickandmorty = p1 + scale_color_rickandmorty()
-p2_rickandmorty = p2 + scale_fill_rickandmorty()
-grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
+
p1_rickandmorty = p1 + scale_color_rickandmorty()
+p2_rickandmorty = p2 + scale_fill_rickandmorty()
+grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)

The Simpsons

This palette is inspired by the colors used in the TV show The Simpsons:

-
p1_simpsons = p1 + scale_color_simpsons()
-p2_simpsons = p2 + scale_fill_simpsons()
-grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
+
p1_simpsons = p1 + scale_color_simpsons()
+p2_simpsons = p2 + scale_fill_simpsons()
+grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)

@@ -401,25 +445,25 @@

Continuous Color Palettes

We will use a correlation matrix visualization (a special type of heatmap) to demonstrate the continuous color palettes in ggsci.

-
library("reshape2")
-
-data("mtcars")
-cor = cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
-cor_melt = melt(cor)
-
-p3 = ggplot(cor_melt,
-            aes(x = Var1, y = Var2, fill = value)) +
-  geom_tile(colour = "black", size = 0.3) +
-  theme_bw() +
-  theme(axis.title.x = element_blank(),
-        axis.title.y = element_blank())
+
library("reshape2")
+
+data("mtcars")
+cor = cor(unname(cbind(mtcars, mtcars, mtcars, mtcars)))
+cor_melt = melt(cor)
+
+p3 = ggplot(cor_melt,
+            aes(x = Var1, y = Var2, fill = value)) +
+  geom_tile(colour = "black", size = 0.3) +
+  theme_bw() +
+  theme(axis.title.x = element_blank(),
+        axis.title.y = element_blank())

GSEA

The GSEA palette (continuous) is inspired by the heatmaps generated by GSEA GenePattern.

-
p3_gsea     = p3 + scale_fill_gsea()
-p3_gsea_inv = p3 + scale_fill_gsea(reverse = TRUE)
-grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
+
p3_gsea     = p3 + scale_fill_gsea()
+p3_gsea_inv = p3 + scale_fill_gsea(reverse = TRUE)
+grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)

@@ -427,38 +471,38 @@

Material Design

The Material Design color palettes are from the material design color guidelines.

We generate a random matrix first:

-
library("reshape2")
-
-set.seed(42)
-k = 9
-x = diag(k)
-x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
-x_melt = melt(x)
-
-p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
-  geom_tile(colour = "black", size = 0.3) +
-  scale_x_continuous(expand = c(0, 0)) +
-  scale_y_continuous(expand = c(0, 0)) +
-  theme_bw() + theme(
-    legend.position = "none", plot.background = element_blank(),
-    axis.line = element_blank(), axis.ticks = element_blank(),
-    axis.text.x = element_blank(), axis.text.y = element_blank(),
-    axis.title.x = element_blank(), axis.title.y = element_blank(),
-    panel.background = element_blank(), panel.border = element_blank(),
-    panel.grid.major = element_blank(), panel.grid.minor = element_blank())
+
library("reshape2")
+
+set.seed(42)
+k = 9
+x = diag(k)
+x[upper.tri(x)] = runif(sum(1:(k - 1)), 0, 1)
+x_melt = melt(x)
+
+p4 = ggplot(x_melt, aes(x = Var1, y = Var2, fill = value)) +
+  geom_tile(colour = "black", size = 0.3) +
+  scale_x_continuous(expand = c(0, 0)) +
+  scale_y_continuous(expand = c(0, 0)) +
+  theme_bw() + theme(
+    legend.position = "none", plot.background = element_blank(),
+    axis.line = element_blank(), axis.ticks = element_blank(),
+    axis.text.x = element_blank(), axis.text.y = element_blank(),
+    axis.title.x = element_blank(), axis.title.y = element_blank(),
+    panel.background = element_blank(), panel.border = element_blank(),
+    panel.grid.major = element_blank(), panel.grid.minor = element_blank())

Plot the matrix with the 19 material design color palettes:

-
grid.arrange(
-  p4 + scale_fill_material("red"),         p4 + scale_fill_material("pink"),
-  p4 + scale_fill_material("purple"),      p4 + scale_fill_material("deep-purple"),
-  p4 + scale_fill_material("indigo"),      p4 + scale_fill_material("blue"),
-  p4 + scale_fill_material("light-blue"),  p4 + scale_fill_material("cyan"),
-  p4 + scale_fill_material("teal"),        p4 + scale_fill_material("green"),
-  p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
-  p4 + scale_fill_material("yellow"),      p4 + scale_fill_material("amber"),
-  p4 + scale_fill_material("orange"),      p4 + scale_fill_material("deep-orange"),
-  p4 + scale_fill_material("brown"),       p4 + scale_fill_material("grey"),
-  p4 + scale_fill_material("blue-grey"),
-  ncol = 6)
+
grid.arrange(
+  p4 + scale_fill_material("red"),         p4 + scale_fill_material("pink"),
+  p4 + scale_fill_material("purple"),      p4 + scale_fill_material("deep-purple"),
+  p4 + scale_fill_material("indigo"),      p4 + scale_fill_material("blue"),
+  p4 + scale_fill_material("light-blue"),  p4 + scale_fill_material("cyan"),
+  p4 + scale_fill_material("teal"),        p4 + scale_fill_material("green"),
+  p4 + scale_fill_material("light-green"), p4 + scale_fill_material("lime"),
+  p4 + scale_fill_material("yellow"),      p4 + scale_fill_material("amber"),
+  p4 + scale_fill_material("orange"),      p4 + scale_fill_material("deep-orange"),
+  p4 + scale_fill_material("brown"),       p4 + scale_fill_material("grey"),
+  p4 + scale_fill_material("blue-grey"),
+  ncol = 6)

From the figure above, we can see that even though an identical matrix was visualized by all plots, some palettes are more preferrable than the others because our eyes are more sensitive to the changes of their saturation levels.

@@ -467,12 +511,12 @@

Non-ggplot2 Graphics

To apply the color palettes in ggsci to other graphics systems (such as base graphics and lattice graphics), simply use the palette generator functions in the table above. For example:

-
mypal = pal_npg("nrc", alpha = 0.7)(9)
-mypal
+
mypal = pal_npg("nrc", alpha = 0.7)(9)
+mypal
## [1] "#E64B35B2" "#4DBBD5B2" "#00A087B2" "#3C5488B2" "#F39B7FB2" "#8491B4B2"
 ## [7] "#91D1C2B2" "#DC0000B2" "#7E6148B2"
-
library("scales")
-show_col(mypal)
+
library("scales")
+show_col(mypal)

You will be able to use the generated hex color codes for such graphics systems accordingly. The transparent level of the entire palette is easily adjustable via the argument "alpha" in every generator or scale function.

diff --git a/docs/articles/index.html b/docs/articles/index.html index 45e5d28..55b0834 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/authors.html b/docs/authors.html index 9942bbf..ee33b3f 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/index.html b/docs/index.html index 9225d82..60da8e8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ ggsci - 2.8.9001 + 2.9 @@ -87,10 +87,10 @@

Installation

Install ggsci from CRAN:

-
install.packages("ggsci")
+
install.packages("ggsci")

Or try the development version on GitHub:

-
# install.packages("devtools")
-devtools::install_github("road2stat/ggsci")
+
# install.packages("devtools")
+devtools::install_github("road2stat/ggsci")

Browse the vignette (or open with vignette("ggsci") in R) for a quick-start guide.

@@ -111,9 +111,9 @@

Changelog

Source: NEWS.md -
+

-ggsci 2.8.9001 (2018-05-07) Unreleased +ggsci 2.9 (2018-05-13) Unreleased

@@ -213,7 +213,7 @@

Contents

    -
  • 2.8.9001
    • +
  • 2.9
  • 2.8
  • 2.7
  • 2.4
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 80e8d0b..279d702 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 1.19.2.1 +pandoc: 2.2.1 pkgdown: 1.0.0 pkgdown_sha: ~ articles: diff --git a/docs/reference/ggsci-package.html b/docs/reference/ggsci-package.html index 43c20e4..c52e98c 100644 --- a/docs/reference/ggsci-package.html +++ b/docs/reference/ggsci-package.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9
diff --git a/docs/reference/index.html b/docs/reference/index.html index 4500cb4..2ad9657 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -65,7 +65,7 @@ ggsci - 2.8.9001 + 2.9

diff --git a/docs/reference/pal_aaas.html b/docs/reference/pal_aaas.html index 20a457d..1ffd4d1 100644 --- a/docs/reference/pal_aaas.html +++ b/docs/reference/pal_aaas.html @@ -70,7 +70,7 @@ ggsci - 2.8.9001 + 2.9
diff --git a/docs/reference/pal_d3.html b/docs/reference/pal_d3.html index 41ecfca..dba78b8 100644 --- a/docs/reference/pal_d3.html +++ b/docs/reference/pal_d3.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9
diff --git a/docs/reference/pal_futurama.html b/docs/reference/pal_futurama.html index c6d4069..142f01e 100644 --- a/docs/reference/pal_futurama.html +++ b/docs/reference/pal_futurama.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_gsea.html b/docs/reference/pal_gsea.html index e2ad0e1..5d744d7 100644 --- a/docs/reference/pal_gsea.html +++ b/docs/reference/pal_gsea.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_igv.html b/docs/reference/pal_igv.html index 8fb3951..c77c524 100644 --- a/docs/reference/pal_igv.html +++ b/docs/reference/pal_igv.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_jama.html b/docs/reference/pal_jama.html index 1937a4f..55b2f18 100644 --- a/docs/reference/pal_jama.html +++ b/docs/reference/pal_jama.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_jco.html b/docs/reference/pal_jco.html index f7a1d4c..444da64 100644 --- a/docs/reference/pal_jco.html +++ b/docs/reference/pal_jco.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_lancet.html b/docs/reference/pal_lancet.html index 700995c..45c95ef 100644 --- a/docs/reference/pal_lancet.html +++ b/docs/reference/pal_lancet.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_locuszoom.html b/docs/reference/pal_locuszoom.html index 8e56bed..6e44561 100644 --- a/docs/reference/pal_locuszoom.html +++ b/docs/reference/pal_locuszoom.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_material.html b/docs/reference/pal_material.html index 954a4c5..707d0f2 100644 --- a/docs/reference/pal_material.html +++ b/docs/reference/pal_material.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_nejm.html b/docs/reference/pal_nejm.html index 9d22669..9043363 100644 --- a/docs/reference/pal_nejm.html +++ b/docs/reference/pal_nejm.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_npg.html b/docs/reference/pal_npg.html index 2054e3b..fe6d9a9 100644 --- a/docs/reference/pal_npg.html +++ b/docs/reference/pal_npg.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_rickandmorty.html b/docs/reference/pal_rickandmorty.html index dbb74bf..5ba3944 100644 --- a/docs/reference/pal_rickandmorty.html +++ b/docs/reference/pal_rickandmorty.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_simpsons.html b/docs/reference/pal_simpsons.html index f75399c..3a5e168 100644 --- a/docs/reference/pal_simpsons.html +++ b/docs/reference/pal_simpsons.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_startrek.html b/docs/reference/pal_startrek.html index f4cb165..5e49363 100644 --- a/docs/reference/pal_startrek.html +++ b/docs/reference/pal_startrek.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_tron.html b/docs/reference/pal_tron.html index 668ee8a..fcc1691 100644 --- a/docs/reference/pal_tron.html +++ b/docs/reference/pal_tron.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/pal_uchicago.html b/docs/reference/pal_uchicago.html index e8c1854..80b41f1 100644 --- a/docs/reference/pal_uchicago.html +++ b/docs/reference/pal_uchicago.html @@ -30,7 +30,7 @@ - + @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 @@ -117,7 +117,7 @@

The University of Chicago Color Palettes

-

Color palettes based on the colors used by The University of Chicago.

+

Color palettes based on the colors used by the University of Chicago.

@@ -143,7 +143,7 @@

Arg

References

-

http://communications.uchicago.edu/identity/color-palette

+

https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf

Examples

diff --git a/docs/reference/pal_ucscgb.html b/docs/reference/pal_ucscgb.html index df63524..16b0bac 100644 --- a/docs/reference/pal_ucscgb.html +++ b/docs/reference/pal_ucscgb.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/rgb_gsea.html b/docs/reference/rgb_gsea.html index 7707b4b..ec871f0 100644 --- a/docs/reference/rgb_gsea.html +++ b/docs/reference/rgb_gsea.html @@ -69,7 +69,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/rgb_material.html b/docs/reference/rgb_material.html index 512b19a..c8cfa65 100644 --- a/docs/reference/rgb_material.html +++ b/docs/reference/rgb_material.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_aaas.html b/docs/reference/scale_aaas.html index 4dea978..ed0c9e8 100644 --- a/docs/reference/scale_aaas.html +++ b/docs/reference/scale_aaas.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 @@ -149,8 +149,8 @@

Arg

Examples

- 
library("ggplot2")
-data("diamonds")
+    
library("ggplot2")
#> Want to understand how all the pieces fit together? Buy the ggplot2
+#> book: http://ggplot2.org/book/
data("diamonds")
 
 ggplot(subset(diamonds, carat >= 2.2),
        aes(x = table, y = price, colour = cut)) +
diff --git a/docs/reference/scale_d3.html b/docs/reference/scale_d3.html
index 73d4c77..7cefe27 100644
--- a/docs/reference/scale_d3.html
+++ b/docs/reference/scale_d3.html
@@ -68,7 +68,7 @@
       
       
         ggsci
-        2.8.9001
+        2.9
       
     

 
diff --git a/docs/reference/scale_futurama.html b/docs/reference/scale_futurama.html
index 23dd835..d872201 100644
--- a/docs/reference/scale_futurama.html
+++ b/docs/reference/scale_futurama.html
@@ -68,7 +68,7 @@
       
       
         ggsci
-        2.8.9001
+        2.9
       
     

 
diff --git a/docs/reference/scale_gsea.html b/docs/reference/scale_gsea.html
index 285a21f..f47081d 100644
--- a/docs/reference/scale_gsea.html
+++ b/docs/reference/scale_gsea.html
@@ -68,7 +68,7 @@
       
       
         ggsci
-        2.8.9001
+        2.9
       
     
 
diff --git a/docs/reference/scale_igv-1.png b/docs/reference/scale_igv-1.png
index 85a89ae..2ebfc13 100644
Binary files a/docs/reference/scale_igv-1.png and b/docs/reference/scale_igv-1.png differ
diff --git a/docs/reference/scale_igv.html b/docs/reference/scale_igv.html
index 8565371..9c3788c 100644
--- a/docs/reference/scale_igv.html
+++ b/docs/reference/scale_igv.html
@@ -68,7 +68,7 @@
       
       
         ggsci
-        2.8.9001
+        2.9
       
     
 
@@ -164,10 +164,12 @@ 
Examp
   geom_histogram(colour = "black", binwidth = 1, position = "dodge") +
   theme_bw()
 
-p1 + scale_color_igv()
p2 + scale_fill_igv()

+p1 + scale_color_igv()
#> Error in grid.Call.graphics(C_setviewport, vp, TRUE): non-finite location and/or size for viewport
p2 + scale_fill_igv()
+
 p1 + scale_colour_manual(
-  values = rep(pal_igv("alternating")(2), times = 3))
p2 + scale_fill_manual(
-  values = rep(pal_igv("alternating")(2), times = 3))
+ values = rep(pal_igv("alternating")(2), times = 3)) +p2 + scale_fill_manual( + values = rep(pal_igv("alternating")(2), times = 3)) diff --git a/docs/reference/scale_jco.html b/docs/reference/scale_jco.html index ee407c7..1a2ac6c 100644 --- a/docs/reference/scale_jco.html +++ b/docs/reference/scale_jco.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_lancet.html b/docs/reference/scale_lancet.html index 85aee3b..b7e097c 100644 --- a/docs/reference/scale_lancet.html +++ b/docs/reference/scale_lancet.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_locuszoom.html b/docs/reference/scale_locuszoom.html index fb25d6f..6cc4289 100644 --- a/docs/reference/scale_locuszoom.html +++ b/docs/reference/scale_locuszoom.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_material.html b/docs/reference/scale_material.html index 5996b0a..17d7b34 100644 --- a/docs/reference/scale_material.html +++ b/docs/reference/scale_material.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_nejm.html b/docs/reference/scale_nejm.html index 62c1da7..bf33c7d 100644 --- a/docs/reference/scale_nejm.html +++ b/docs/reference/scale_nejm.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_npg.html b/docs/reference/scale_npg.html index 2a8e375..974133b 100644 --- a/docs/reference/scale_npg.html +++ b/docs/reference/scale_npg.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_rickandmorty.html b/docs/reference/scale_rickandmorty.html index dfd1045..7c0a76e 100644 --- a/docs/reference/scale_rickandmorty.html +++ b/docs/reference/scale_rickandmorty.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_simpsons.html b/docs/reference/scale_simpsons.html index 4f21c6c..7042c1a 100644 --- a/docs/reference/scale_simpsons.html +++ b/docs/reference/scale_simpsons.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_startrek.html b/docs/reference/scale_startrek.html index 6c44af4..a2f9a48 100644 --- a/docs/reference/scale_startrek.html +++ b/docs/reference/scale_startrek.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_tron.html b/docs/reference/scale_tron.html index 147ee4d..da41096 100644 --- a/docs/reference/scale_tron.html +++ b/docs/reference/scale_tron.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 diff --git a/docs/reference/scale_uchicago.html b/docs/reference/scale_uchicago.html index 94b61ee..5095cea 100644 --- a/docs/reference/scale_uchicago.html +++ b/docs/reference/scale_uchicago.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9 @@ -153,7 +153,7 @@

Arg

References

-

http://communications.uchicago.edu/identity/color-palette

+

https://news.uchicago.edu/sites/default/files/attachments/_uchicago.identity.guidelines.pdf

Examples

diff --git a/docs/reference/scale_ucscgb.html b/docs/reference/scale_ucscgb.html index cb1719d..92ac2c0 100644 --- a/docs/reference/scale_ucscgb.html +++ b/docs/reference/scale_ucscgb.html @@ -68,7 +68,7 @@ ggsci - 2.8.9001 + 2.9