跟着Oncogene学作图：R语言gggenomes画桑基图（共线性图）

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发布于 2023-01-06 20:25:03

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发布于 2023-01-06 20:25:03

文章被收录于专栏：小明的数据分析笔记本小明的数据分析笔记本

论文

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma

https://www.nature.com/articles/s41388-021-02054-3

这个是公众号读者的留言，问下图如何实现

image.png

论文中没有提供数据和代码，我们简单构造一个示例数据，然后代码自己写

这个图可以用桑基图的画法来做，之前的推文介绍了两个桑基图的做法

今天的推文介绍一下gggenomes这个R包，这个是用来做基因组共线性的图的，但是共线性和桑基图看起来效果是一样的，所以桑基图也可以用这个来做

github主页

https://github.com/thackl/gggenomes

安装代码

devtools::install_github("thackl/gggenomes")

安装过程会更新很多R包，会遇到一些报错，自己搜索报错提示信息应该能够解决

首先是一个简单的小例子

示例数据

image.png

读取数据作图

library(readxl)
library(gggenomes)

df<-read_excel("gggenomes_examples.xlsx",
               sheet="Sheet1")
df
gggenomes(genes = df)+
  geom_gene()

gggenomes(genes = df)+
  geom_gene(shape=0,aes(fill=group))

image.png

添加两个图之间的阴影

image.png

dflink<-read_excel("gggenomes_examples.xlsx",sheet = "Sheet2")
dflink
gggenomes(genes = df,links = dflink)+
  geom_link(offset = 0.05,aes(fill=group2))+
  geom_gene(shape=0,aes(fill=group),size=5)+
  theme(legend.position = "none")

image.png

接下来是模仿论文中的那个图

示例数据

image.png

读取数据并作图

dflink<-read_excel("gggenomes_examples.xlsx",sheet = "Sheet2")
dflink
gggenomes(genes = df,links = dflink)+
  geom_link(offset = 0.05,aes(fill=group2))+
  geom_gene(shape=0,aes(fill=group),size=5)+
  theme(legend.position = "none")

df3<-read_excel("gggenomes_examples.xlsx",
                sheet = "Sheet3")
df3


df3 %>% 
  filter(seq_id=="Normal") %>% 
  mutate(length=end-start+1) -> dflink01

df3 %>% 
  filter(seq_id=="Tumor") %>% 
  mutate(length=end-start+1) -> dflink02

bind_cols(dflink01,dflink02) -> dflinks
colnames(dflinks)<-c(c("seq_id","start","end","group",'length'),
                     paste0(c("seq_id","start","end","group",'length'),2))
dflinks
gggenomes(genes=df3,links = dflinks)+
  geom_bin_label(size=5)+
  geom_link(aes(fill=group),offset = 0.3)+
  geom_gene(aes(fill=group),shape=0,
            size=10)+
  theme(legend.position = "none",
        axis.line.x = element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.x = element_blank())+
  xlim(-15,100)+
  scale_fill_manual(values =as.vector(tidyquant::palette_dark()))+
  annotate(geom = "segment",
           x=0,xend = 100,y = 0.5,yend=0.5)+
  geom_segment(data=data.frame(x=c(0,50,100),
                               xend=c(0,50,100),
                               y=c(0.5,0.5,0.5),
                               yend=c(0.4,0.4,0.4)),
               aes(x=x,xend=xend,y=y,yend=yend),
               inherit.aes = FALSE)+
  geom_text(data=data.frame(x=c(0,50,100),
                            y=c(0.4,0.4,0.4),
                            label=c("0.0",'0.5','1.0')),
            aes(x=x,y=y,label=label),vjust=1)

image.png

最后是制作封面图

gggenomes(genes=df3,links = dflinks)+
  geom_bin_label(size=5)+
  geom_link(aes(fill=group),offset = 0.3)+
  geom_gene(aes(fill=group),shape=0,
            size=10)+
  theme(legend.position = "none",
        axis.line.x = element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.x = element_blank())+
  xlim(-15,100)+
  scale_fill_manual(values =as.vector(tidyquant::palette_dark()))+
  annotate(geom = "segment",
           x=0,xend = 100,y = 0.5,yend=0.5)+
  geom_segment(data=data.frame(x=c(0,50,100),
                               xend=c(0,50,100),
                               y=c(0.5,0.5,0.5),
                               yend=c(0.4,0.4,0.4)),
               aes(x=x,xend=xend,y=y,yend=yend),
               inherit.aes = FALSE)+
  geom_text(data=data.frame(x=c(0,50,100),
                            y=c(0.4,0.4,0.4),
                            label=c("0.0",'0.5','1.0')),
            aes(x=x,y=y,label=label),vjust=1) -> p1

gggenomes(genes=df3,links = dflinks)+
  geom_bin_label(size=5)+
  geom_link(aes(fill=group),offset = 0.3)+
  geom_gene(aes(fill=group),shape=0,
            size=10)+
  theme(legend.position = "none",
        axis.line.x = element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.x = element_blank())+
  xlim(-15,100)+
  scale_fill_manual(values =as.vector(tidyquant::palette_light())) -> p2

library(patchwork)

p2/p1