论文
The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution
https://www.nature.com/articles/s41477-022-01187-x#Sec21
本地pdf s41477-022-01187-x.pdf
论文中的数据基本都公开了，我们可以利用论文中的数据模仿论文中的图，今天的推文模仿一下论文中Figure1c 和 figure1f
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figure1c
部分示例数据截图
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读取数据并作图
library(readxl) datf3c<-read_excel("data/20220807/41477_2022_1187_MOESM4_ESM.xlsx", sheet = "Fig.1C", skip = 1) head(datf3c) library(tidyverse) datf3c %>% select(-'4dTV_1') %>% pivot_longer(-'4dTV_2') %>% mutate(name = fct_relevel(name,c("Acorus-Acorus", "Acorus-Zostera", "Acorus-Oryza", "Acorus-Asparagus"))) -> new.datf3c #install.packages("latex2exp") library(latex2exp) ggplot(data=new.datf3c, aes(x=`4dTV_2`,y=value,color=name))+ geom_line(size=1)+ scale_color_manual(values = c("#ff0000","#7030a0", "#00b050","#5b9bd5"), name=NULL)+ theme_classic()+ theme(legend.position = c(0.8,0.8), legend.text = element_text(face = "italic"))+ scale_x_continuous(expand = expansion(mult = c(0,0)), limits = c(0,2), breaks = seq(0,2,0.2))+ scale_y_continuous(expand = expansion(mult = c(0,0)), limits = c(0,300))+ labs(x="4dTV",y="No.of gene pairs") -> p1 p1 
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figure1f
部分示例数据截图
image.png
读取数据并作图
datf3f<-read_excel("data/20220807/41477_2022_1187_MOESM4_ESM.xlsx", sheet = "Fig.1F", skip = 1) head(datf3f) datf3f %>% pivot_longer(-"Distance to Gene Start") %>% ggplot(aes(x=`Distance to Gene Start`, y=value, color=name))+ geom_line()+ scale_color_manual(values = c("#ff0000","#00b0f0"))+ theme_classic()+ theme(legend.position = c(0.9,0.2), plot.margin = unit(c(0.1,0.5,0.1,0.1),'cm'), legend.title = element_blank())+ scale_x_continuous(expand = expansion(mult = c(0,0)), labels = c("-2 kb","Start","", "Stop","+2 kb"))+ scale_y_continuous(expand = expansion(mult = c(0,0)), limits = c(0,0.4))+ labs(x=NULL,y="Ratio of TEs") -> p2 p2 
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最后是拼图
p1+p2+ plot_annotation(tag_levels = list(c("c","f"))) 
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示例数据可以在论文中去下载，代码直接在推文中复制，如果需要我整理好的数据和代码可以给推文打赏1元获取
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