1. ggsci介绍
ggsci提供了一系列配置好的颜色给ggplot2绘制出的图片调色，包括一些知名杂志期刊或者软件甚至是知名科幻电影、动画等的经典配色风格。将这些配色风格直接应用于我们绘制出的图，方便又好看。
# 下载
# download ggsci package
install.packages("ggsci")
#install.packages("devtools")
devtools::install_github("nanxstats/ggsci")
对所有的调色板，使用方法：p+scale_color_xx()和p+scale_fill_xx()。
p是绘制好的ggplot图，xx指调色板的名字
所有调色板的名字：npg, aaas, nejm, lancet, jama, jco, ucscgb, d3, locuszoom, igv, cosmic, uchicago, startrek, tron, futurama, rickandmorty, simpsons, gsea, material
2. ggsci使用
2.1 离散型调色板，应用于离散型数值
使用diamond数据集做演示，先使用diamond数据集绘制两张图
library("ggsci")
library("ggplot2")
library("gridExtra")
library("patchwork")
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()
p1|p2
- NPG（将NPG杂志的配色风格应用到刚刚绘制的两张图）
p1_npg <- p1 + scale_color_npg()
p2_npg <- p2 + scale_fill_npg()
grid.arrange(p1_npg, p2_npg, ncol = 2)
颜色提取
show_col(pal_npg("nrc", alpha = 0.6)(10))
##上面palette=c('nrc)，所以取颜色时pal_npg()第一个参数就是‘nrc’。如果是‘Default’就填‘Default’，其它的函数都是一样的取法。
- AAAS（使用AAAS杂志的配色风格）
p1_aaas <- p1 + scale_color_aaas()
p2_aaas <- p2 + scale_fill_aaas()
grid.arrange(p1_aaas, p2_aaas, ncol = 2)
- NEJM（新英格兰配色风格）
p1_nejm <- p1 + scale_color_nejm()
p2_nejm <- p2 + scale_fill_nejm()
grid.arrange(p1_nejm, p2_nejm, ncol = 2)
- Lancet
p1_lancet <- p1 + scale_color_lancet()
p2_lancet <- p2 + scale_fill_lancet()
grid.arrange(p1_lancet, p2_lancet, ncol = 2)
- JAMA
p1_jama <- p1 + scale_color_jama()
p2_jama <- p2 + scale_fill_jama()
grid.arrange(p1_jama, p2_jama, ncol = 2)
- JCO
p1_jco <- p1 + scale_color_jco()
p2_jco <- p2 + scale_fill_jco()
grid.arrange(p1_jco, p2_jco, ncol = 2)
- UCSCGB
p1_ucscgb <- p1 + scale_color_ucscgb()
p2_ucscgb <- p2 + scale_fill_ucscgb()
grid.arrange(p1_ucscgb, p2_ucscgb, ncol = 2)
- D3
p1_d3 <- p1 + scale_color_d3()
p2_d3 <- p2 + scale_fill_d3()
grid.arrange(p1_d3, p2_d3, ncol = 2)
- LocusZoom
p1_locuszoom <- p1 + scale_color_locuszoom()
p2_locuszoom <- p2 + scale_fill_locuszoom()
grid.arrange(p1_locuszoom, p2_locuszoom, ncol = 2)
- IGV
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
p1_uchicago <- p1 + scale_color_uchicago()
p2_uchicago <- p2 + scale_fill_uchicago()
grid.arrange(p1_uchicago, p2_uchicago, ncol = 2)
- Star Trek
p1_startrek <- p1 + scale_color_startrek()
p2_startrek <- p2 + scale_fill_startrek()
grid.arrange(p1_startrek, p2_startrek, ncol = 2)
- Tron Legend
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
p1_futurama <- p1 + scale_color_futurama()
p2_futurama <- p2 + scale_fill_futurama()
grid.arrange(p1_futurama, p2_futurama, ncol = 2)
- Rick and Morty（我非常喜欢的动漫）
p1_rickandmorty <- p1 + scale_color_rickandmorty()
p2_rickandmorty <- p2 + scale_fill_rickandmorty()
grid.arrange(p1_rickandmorty, p2_rickandmorty, ncol = 2)
- The Simpsons
p1_simpsons <- p1 + scale_color_simpsons()
p2_simpsons <- p2 + scale_fill_simpsons()
grid.arrange(p1_simpsons, p2_simpsons, ncol = 2)
2.2 连续型调色板
使用mtcars数据集做演示
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
将GSEA的配色风格应用到刚刚绘制的图
p3_gsea <- p3 + scale_fill_gsea()
p3_gsea_inv <- p3 + scale_fill_gsea(reverse = TRUE)
grid.arrange(p3_gsea, p3_gsea_inv, ncol = 2)
