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跟着Nature Communications学作图：R语言ggplot2画图展示捐赠者的临床概况

2023-02-19 12:27:47 时间

论文

Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue

https://www.nature.com/articles/s41467-022-33663-5#Sec18

今天的推文我们重复一下论文中的Figure1a，看起来非常像一个表格，很有意思

image.png

我们使用ggplot2来实现，主要分为三个部分，文本，形状，和背景的灰色条

首先是文本的部分数据截图

image.png

形状的三个数据截图

image.png

背景灰色条数据截图

image.png

总共5份数据，放在同一个excel文件里，5个不同的子表格

读取数据并作图 

library(readxl)
library(ggplot2)
library(stringr)
library(tidyverse)

dat01<-read_excel("data/20221009/example_data.xlsx",
                sheet = "Sheet1")
dat01 %>% 
  mutate(label01=case_when(
    length(label) == 7 ~ str_pad(label,8,"right"),
    TRUE ~ label
  )) -> new.dat01

new.dat01

dat02<-read_excel("data/20221009/example_data.xlsx",
                  sheet = "Sheet2")
dat02

dat03<-read_excel("data/20221009/example_data.xlsx",
                  sheet = "Sheet3")
dat03

dat04<-read_excel("data/20221009/example_data.xlsx",
                  sheet = "Sheet4")
dat04

dat05<-read_excel("data/20221009/example_data.xlsx",
                  sheet = "Sheet5")
dat05

x_labels<-c("","Age","Normal\nTissue","Tissue\nSubtype",
            "Treatment\ntype","Treatment\ncycli",
            "Sampling after\ntreatment\n(months)",
            "Seqenced\nsamples")
ggplot()+
  scale_x_continuous(limits = c(0.5,8),
                     breaks = 1:8,
                     labels = x_labels,
                     position = "top")+
  geom_text(data=new.dat01,aes(x=x,y=y,label=label01))+
  geom_point(data=dat02,aes(x=x,y=y,color=`Normal tissue type`),
             size=5)+
  scale_color_manual(values = c("Colon"="#d38e91",
                                "Liver"="#1f639a"))+
  ggnewscale::new_scale_color()+
  geom_point(data=dat03,aes(x=x,y=y,color=`Tissue subtype`),
             size=5)+
  scale_color_manual(values = c("Descending colon"="#f6d65b",
                                "Sigmoid"="#3eada2",
                                "Rectum"="#eb553a",
                                "Liver"="#206599"))+
  ggnewscale::new_scale_color()+
  geom_point(data=dat04,aes(x=x,y=y,color=Treatment),
             size=5,shape=15)+
  scale_color_manual(values = c("5-FU + platinum"="#f49b5e",
                                "5-FU + radiation"="#c44657",
                                "5-FU + platinum + radiation"=
                                  "#89520e"))+
  theme_bw()+
  theme(axis.title = element_blank(),
        panel.grid = element_blank(),
        panel.border = element_blank(),
        axis.text.y = element_blank(),
        axis.ticks = element_blank(),
        axis.text.x = element_text(hjust=0.5,vjust=0.5))+
  geom_rect(data=dat05,
            aes(xmin=-Inf,xmax=Inf,ymin=ymin,ymax=ymax),
            fill="gray",alpha=0.2)

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