跟着Nature Plants学作图：R语言ggplot2分组散点图添加置信区间/图片上插入表格

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发布于 2024-04-03 20:32:42

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发布于 2024-04-03 20:32:42

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

Heritable microbiome variation is correlated with source environment in locally adapted maize varieties

https://www.nature.com/articles/s41477-024-01654-7

论文中提供了作图用到的原始数据，我们可以试着用原始数据复现论文中的图，今天的推文我们来复现一下论文中的Figure1a

image.png

今天推文比较重要的知识点是

分组添加置信椭圆
在图片上插入表格

插入表格主要想实现上图文字的效果：插入多行文字，有的文字是常规字体，有的文字带斜体上下标这种

参考这个链接 https://cran.r-project.org/web/packages/gridExtra/vignettes/tableGrob.html

部分示例数据

image.png

加载需要用到的R包

library(readxl)
library(tidyverse)
library(gridExtra)

gridExtra用来在图片上插入表格

读取数据

read_excel("D:/R_4_1_0_working_directory/env001/data/20240322/41477_2024_1654_MOESM4_ESM.xlsx",
           sheet = "Fig1a") -> fig1a.dat

作图代码

fig1a.dat %>% 
  filter(Compartment=="Rhizosphere") %>% 
  ggplot(aes(x=CAP1,y=CAP2))+
  geom_point(aes(fill=Treatment),
             shape=21,size=5,
             color="gray",
             alpha=0.8)+
  stat_ellipse(aes(group = Treatment), 
               size = 0.5, 
               level = 0.95,
               show.legend = F,
               lty="dashed")+
  labs(x="CAP1 (22.6%)",y="CAP2 (6.8%)")+
  theme_bw(base_size = 15)+
  theme(panel.grid = element_blank(),
        panel.border = element_blank(),
        axis.line = element_line())+
  annotate(geom="text",x=-0.2,y=0.3,
           label="Rhizosphere bacteria",
           size=5,hjust=0)-> plot.a1
plot.a1

image.png

(论文中的图的配色不是很好看，这里就不改配色了)

添加表格

plot.a1 +
  annotation_custom(tableGrob(mytable,rows = NULL,cols = NULL,
                              theme = ttheme_minimal(core=list(fg_params=list(hjust=0,
                                                                              parse=TRUE,
                                                                              x=0,
                                                                              fontsize=15)))),
                    xmin=0.25, xmax=0.3, ymin=0, ymax=0.3)

image.png

第二个图也是一样的代码

fig1a.dat %>% 
  filter(Compartment=="Root") %>% 
  ggplot(aes(x=CAP1,y=CAP2))+
  geom_point(aes(fill=Treatment),
             shape=22,size=5,
             color="gray",
             alpha=0.8)+
  stat_ellipse(aes(group = Treatment), 
               size = 0.5, 
               level = 0.95,
               show.legend = F,
               lty="dashed")+
  labs(x="CAP1 (22.6%)",y="CAP2 (6.8%)")+
  theme_bw(base_size = 15)+
  theme(panel.grid = element_blank(),
        panel.border = element_blank(),
        axis.line = element_line())+
  annotate(geom="text",x=-0.2,y=0.3,
           label="Rhizosphere bacteria",
           size=5,hjust=0)+
  xlim(NA,1.1)+
  annotation_custom(tableGrob(mytable,rows = NULL,cols = NULL,
                              theme = ttheme_minimal(core=list(fg_params=list(hjust=0,
                                                                              parse=TRUE,
                                                                              x=0,
                                                                              fontsize=15)))),
                    xmin=1.05, xmax=1.1, ymin=0, ymax=0.3) -> plot.a2

组合图

library(patchwork)
pdf(file = "Rplot2.pdf",width = 18.8,height = 8)
plot.a1+plot.a2+
  plot_layout(guides="collect")& theme(legend.position = 'bottom')
dev.off()