ixxmu
commented
1 year ago 跟着Nature Communications学作图：R语言ggplot2箱线图/抖动散点图展示多物种基因组大小和TE含量 by 小明的数据分析笔记本
论文
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits
https://www.nature.com/articles/s41467-020-18795-w
s41467-020-18795-w.pdf
这个是是有读者在公众号后台留言问到
我把论文找来看了一下，论文对应的图大部分都有数据，我们可以试着复现其中的图，先从最简单的的开始，论文中的Figure2是箱线图加抖动散点图，论文的配色也很好看，可以保留作为自己配色备选
部分示例数据截图
首先是读取数据
library(tidyverse)
dat<-read_delim("data/20230909/Source Data/Source_Data_figure_1a.csv",
delim = ",")
colnames(dat)
dat %>%
pull(Ecology) %>%
table()
左侧的图展示基因组大小，代码如下
ggplot(data=dat %>%
filter(Ecology!="Yeast"&Ecology!="Parasite") %>%
mutate(Ecology=factor(Ecology,levels = c("Wood decayer",
"Endophyte",
"Arbuscular mycorrhizae",
"Orchid mycorrhizae",
"Ericoid mycorrhizae",
"Pathogen",
"Saprotroph",
"Ectomycorrhizae"))),
aes(x=Genome.size,y=Ecology))+
geom_boxplot(color="gray")+
geom_jitter(aes(color=Ecology),
size=5,
show.legend = FALSE,
alpha=0.5)+
scale_color_manual(values = c("#f1a2c9","#b6b3b3","#a8e3ea",
"#fde05f","#f49b40",
"#7ac84e","#73a1cb","#e15e53"))+
scale_x_continuous(limits = c(0,150000000),
labels = function(x){x/1000000})+
theme_bw()+
theme(panel.border = element_blank(),
axis.ticks = element_blank())+
labs(x=NULL,y=NULL,title = "Genomes (Mbp)")
右侧的图代码基本一样
ggplot(data=dat %>%
filter(Ecology!="Yeast"&Ecology!="Parasite") %>%
mutate(Ecology=factor(Ecology,levels = c("Wood decayer",
"Endophyte",
"Arbuscular mycorrhizae",
"Orchid mycorrhizae",
"Ericoid mycorrhizae",
"Pathogen",
"Saprotroph",
"Ectomycorrhizae"))),
aes(x=TE.CoverageTotal,y=Ecology))+
geom_boxplot(color="gray")+
geom_jitter(aes(color=Ecology),
size=5,
show.legend = FALSE,
alpha=0.5)+
scale_color_manual(values = c("#f1a2c9","#b6b3b3","#a8e3ea",
"#fde05f","#f49b40",
"#7ac84e","#73a1cb","#e15e53"))+
scale_x_continuous(limits = c(0,100))+
theme_bw()+
theme(panel.border = element_blank(),
axis.ticks = element_blank(),
axis.text.y = element_blank())+
labs(x=NULL,y=NULL,title = "Repeat element coverage (%)")
最后是拼图
library(patchwork)
p1+p2
示例数据可以到论文中下载，代码可以在推文中复制，或者给推文打赏一元获取我整理好的数据和代码
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小明的数据分析笔记本
小明的数据分析笔记本 公众号 主要分享：1、R语言和python做数据分析和数据可视化的简单小例子；2、园艺植物相关转录组学、基因组学、群体遗传学文献阅读笔记；3、生物信息学入门学习资料及自己的学习笔记！
https://mp.weixin.qq.com/s/8kk04B3ptyhDLRhcdIIf0g