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
  <dbl> <ord>     <ord> <ord>   <dbl> <dbl> <int> <dbl> <dbl> <dbl>
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。

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。

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