ggsci_cover.jpg
R科研绘图调色板—ggsci包
简介
ggsci
ggsci提供了一系列高质量的调色板，其灵感来自于期刊、电影等。ggsci中的调色板可用于ggplot2。基本用法：
scale_color_palname()scale_fill_palname()
#安装并加载ggsci包
install.packages("ggsci")
library("ggsci")
library("ggplot2")
library("gridExtra")
离散型调色板
使用散点图和条形图来演示ggsci中的调色板。
#示例数据集
data("diamonds")#使用diamonds数据集
head(diamonds)
> head(diamonds)
# A tibble: 6 x 10
carat cut color clarity depth table price x y z
1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
4 0.290 Premium I VS2 62.4 58 334 4.2 4.23 2.63
5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
#原始配色
p1 <- ggplot(
subset(diamonds, carat >= 2.2), #筛选数据
aes(x = table, y = price, colour = cut) #确定xy
) +
geom_point(alpha = 0.7) + #画点
geom_smooth(method = "loess", alpha = 0.05, size = 1, span = 1) + #画平滑曲线
theme_bw() #主题
p2 <- ggplot(
subset(diamonds, carat > 2.2 & depth > 55 & depth < 70), #筛选数据
aes(x = depth, fill = cut) #确定x
) +
geom_histogram(colour = "black", binwidth = 1, position = "dodge") + #画直方图
theme_bw() #主题
grid.arrange(p1, p2, ncol = 2) #合并两图
origin
Nature配色
p1_npg <- p1 + scale_color_npg()
p2_npg <- p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
NPG
美国科学促进会(AAAS)
p1_aaas <- p1 + scale_color_aaas()
p2_aaas <- p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
AAAS
新英格兰杂志(NEJM)
p1_lancet <- p1 + scale_color_lancet()
p2_lancet <- p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
NEJM
柳叶刀(Lancet)
p1_lancet <- p1 + scale_color_lancet()
p2_lancet <- p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
LANCET
美国医学会杂志(JAMA)
p1_jama <- p1 + scale_color_jama()
p2_jama <- p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
JAMA
临床肿瘤学杂志(JCO)
p1_jco <- p1 + scale_color_jco()
p2_jco <- p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
JCO
创：战纪(Tron Legacy)
比较适用于使用黑暗主题。
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)
Tron Legacy
辛普森(The Simpsons)
p1_simpsons <- p1 + scale_color_simpsons()
p2_simpsons <- p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
The Simpsons
连续型调色板
用相关性热图来展示。
library("reshape2")
data("mtcars") #示例数据
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()
)
Continuous Color Palettes
GSEA
GSEA调色板的灵感来自GSEA GenePattern生成的热图。
p3_gsea <- p3 + scale_fill_gsea()
p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
GSEA_COLOR
Material Design
The Material Design color palettes are from the material design color guidelines.
先生成一个随机矩阵
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()
)
用19种Material Design调色板绘制矩阵:
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
)
Material Design
非ggplot图
如果不是··作的图，可以直接调用颜色参数。
mypal <- pal_npg("nrc", alpha = 0.7)(9)
mypal
library("scales")
show_col(mypal)
mypal
总结
下表总结了所有可用的调色板。
| Name | Scales | Palette Types | Palette Generator |
|---|---|---|---|
| NPG | scale_color_npg() scale_fill_npg() |
"nrc" |
pal_npg() |
| AAAS | scale_color_aaas() scale_fill_aaas() |
"default" |
pal_aaas() |
| NEJM | scale_color_nejm() scale_fill_nejm() |
"default" |
pal_nejm() |
| Lancet | scale_color_lancet() scale_fill_lancet() |
"lanonc" |
pal_lancet() |
| JAMA | scale_color_jama() scale_fill_jama() |
"default" |
pal_jama() |
| JCO | scale_color_jco() scale_fill_jco() |
"default" |
pal_jco() |
| UCSCGB | scale_color_ucscgb() scale_fill_ucscgb() |
"default" |
pal_ucscgb() |
| D3 | scale_color_d3() scale_fill_d3() |
"category10" "category20" "category20b" "category20c" |
pal_d3() |
| LocusZoom | scale_color_locuszoom() scale_fill_locuszoom() |
"default" |
pal_locuszoom() |
| IGV | scale_color_igv() scale_fill_igv() |
"default" "alternating" |
pal_igv() |
| COSMIC | scale_color_cosmic() scale_fill_cosmic() |
"hallmarks_light" "hallmarks_dark" "signature_substitutions" |
pal_cosmic() |
| UChicago | scale_color_uchicago() scale_fill_uchicago() |
"default" "light" "dark" |
pal_uchicago() |
| Star Trek | scale_color_startrek() scale_fill_startrek() |
"uniform" |
pal_startrek() |
| Tron Legacy | scale_color_tron() scale_fill_tron() |
"legacy" |
pal_tron() |
| Futurama | scale_color_futurama() scale_fill_futurama() |
"planetexpress" |
pal_futurama() |
| Rick and Morty | scale_color_rickandmorty() scale_fill_rickandmorty() |
"schwifty" |
pal_rickandmorty() |
| The Simpsons | scale_color_simpsons() scale_fill_simpsons() |
"springfield" |
pal_simpsons() |
| 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() |
参考
https://nanx.me/ggsci/articles/ggsci.html
代码领取：后台回复"ggsci"即可领取完整代码。
往期内容：
单细胞转录组|Seurat 4.0 使用指南
R绘图实战|GSEA富集分析图