柱状图

R版本与运行环境信息

Date:2021-7-22
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

柱状图

library(tidyverse)
library(ggsci)
library(ggbreak)
plot_theme <- 
  theme_bw()+
  theme(axis.title.x = element_text(size = 18),
        axis.title.y = element_text(size = 18),
        axis.text = element_text(size = 13,color = "black"))
#数据集为三个不同地点的物种组成数据
setwd("G:\\Desktop\\s_note\\data\\plot")
df <- read_csv("df2.csv")
> df
# A tibble: 27 x 4
   group  Phylum              mean       sd
   <chr>  <chr>              <dbl>    <dbl>
 1 site_A Acidobacteria    0.0665  0.0139  
 2 site_A Actinobacteria   0.0720  0.0151  
 3 site_A Bacteroidetes    0.143   0.0218  
 4 site_A Chloroflexi      0.0239  0.00538 
 5 site_A Firmicutes       0.0529  0.0227  
 6 site_A Gemmatimonadetes 0.0416  0.00800 
 7 site_A Oxyphotobacteria 0.00199 0.000669
 8 site_A Proteobacteria   0.590   0.0318  
 9 site_A others           0.00822 0.00177 
10 site_B Acidobacteria    0.0862  0.0111  
# ... with 17 more rows

分组柱状图和堆积图

分组柱状图

#errorbar和bar以及point的 position_dodge() 要一样，否则会重叠
ggplot(df) + 
  geom_bar(aes(group,mean,fill = Phylum),
                      stat = "identity",
                      position = position_dodge(0.75),width = 0.8) + 
  geom_errorbar(aes(group,sd,ymax = mean + sd,ymin = mean -sd,group = Phylum),
                position = position_dodge(0.75),
                alpha = 0.75,
                width = 0.5,
                size = 0.73) + 
  scale_fill_npg() +
  geom_point(aes(group,mean,color = Phylum),
                          position = position_dodge(0.75)) + 
  scale_color_npg() +
  labs(y = "Relative abundance(%)",x = "Site")+
  ggtitle("Test of bar")+
  plot_theme

堆积图

#将position_dodge改为position_fill即可
ggplot(df) + 
  geom_bar(aes(group,mean,fill = Phylum),
           stat = "identity",
           position = position_fill(0.5),width = 0.3) +
  scale_fill_npg() + 
  labs(y = "Relative abundance(%)",x = "Site")+
  plot_theme