本文主要展示如何利用R语言绘制来自nature期刊Genetic and chemotherapeutic influences on germline hypermutation（Joanna Kaplanis, et al,2022）[1]一文中的Extended Data Fig1.b。该图形式为热图，并添加了标签。如下图所示：
1、图形绘制
library(tidyverse)
#构造数据
GEL.df <-
data.frame(
"GEL" = paste0("GEL_", 1:11),
"C>A" = runif(11, 0, 18),
"C>G" = runif(11, 0, 6),
"C>T" = runif(11, 0, 5),
"CpG>TpG" = runif(11, 0, 8),
"T>A" = runif(11, 0, 11),
"T>C" = runif(11, 0, 16),
"T>G" = runif(11, 0, 16)) %>%
reshape2::melt(id.vars = "GEL", variable.name = "variable", value.name = "value")
GEL.df$value <- round(GEL.df$value, digits = 2)
head(GEL.df)
# GEL variable value
#1 GEL_1 C.A 7.03
#2 GEL_2 C.A 14.49
#3 GEL_3 C.A 3.07
#4 GEL_4 C.A 10.50
#5 GEL_5 C.A 9.34
#6 GEL_6 C.A 12.67
str(GEL.df)
#'data.frame': 77 obs. of 3 variables:
#$ GEL : chr "GEL_1" "GEL_2" "GEL_3" "GEL_4" ...
#$ variable: Factor w/ 7 levels "C.A","C.G","C.T",..: 1 1 1 1 1 1 1 1 1 1 ...
#$ value : num 7.03 14.49 3.07 10.5 9.34 ...
#绘图
ggplot(GEL.df,aes(variable, GEL, fill = value)) +
geom_tile() +
geom_text(aes(label = value)) +
scale_fill_distiller(palette = "Purples", direction = 1, breaks = seq(0, 20, 5), limits = c(0, 20)) +
theme_minimal() +
theme(axis.title = element_blank(),
axis.text = element_text(size = 12, colour = "black"),
legend.title = element_text(size = 13),
legend.text = element_text(size = 12),
axis.text.x = element_text(angle = 90, hjust = 0)) +
scale_x_discrete(position = "top") +
labs(fill = "−log10[P]")
该图绘图形式较为简洁，一个需要注意的地方是x轴的坐标轴标签位于上方，因此需要用到scale_x_discrete() 函数，设置其中的position参数即可。
2、其他
其他绘图方法可进一步阅读公众号其他文章。
如有帮助请多多点赞哦！
参考资料
Kaplanis, J., Ide, B., Sanghvi, R. et al. Genetic and chemotherapeutic influences on germline hypermutation. Nature 605, 503–508 (2022). : https://doi.org/10.1038/s41586-022-04712-2
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