跟着Nature microbiology学作图：R语言ggplot2分组箱线图/wilcox秩和检验

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



datj<-read_excel("data/20230305/41564_2022_1270_MOESM6_ESM.xlsx",
                 sheet = "Fig3j")
head(datj)
colnames(datj)

p<-ggplot(data=datj,aes(x=`ID type`,
                     y=log10(`IS region proportion`)))+
  geom_boxplot(aes(fill=Database),
               outlier.shape = 1,
               outlier.colour = "gray",
               outlier.alpha = 0.2)+
  theme_bw()+
  theme(panel.grid = element_blank(),
        axis.text.x = element_text(angle=60,hjust=1,vjust=1),
        legend.position = "bottom")+
  scale_fill_manual(values = c("IMGG"="#1b9e77",
                               "UHGG"="#d95f02"),
                    name=NULL)+
  labs(x=NULL,y="IS region proportion")+
  scale_y_continuous(breaks = c(-2,-1,0),
                     labels = c("0.01","0.10","1.00"))
p

ggplot_build(p)$data[[1]] %>% select(x,ymin,ymax) -> errorbar.df



p.bottom<-p+
  geom_segment(data = errorbar.df,
               aes(x=x-0.15,xend=x+0.15,y=ymin,yend=ymin))+
  geom_segment(data = errorbar.df,
               aes(x=x-0.15,xend=x+0.15,y=ymax,yend=ymax))

p.bottom

datj %>% 
  pull(`ID type`) %>% 
  unique() -> group.info

pvalue.df<-tibble(x=character(),
               pvalue=numeric())

for(info in group.info){
  datj %>% 
    filter(`ID type`==info) -> tmp.df
  wilcox.test(`IS region proportion`~`Database`,
              data=tmp.df) -> a
  add_row(pvalue.df,
          x=info,
          pvalue=a$p.value) -> pvalue.df
}

min_p<-min(pvalue.df %>% filter(pvalue !=0) %>% 
      pull(pvalue))
pvalue.df %>% 
  mutate(new_p=case_when(
    pvalue == 0 ~ min_p,
    TRUE ~ pvalue
  )) ->pvalue.df

library(RColorBrewer)
scale_color_distiller()
p.top<-ggplot(data = pvalue.df,aes(x=x,y=1))+
  geom_point(size=5,shape=15,
             aes(color=-log10(new_p)))+
  scale_color_distiller(palette = "Greys",
                        direction = 1,
                        name="-log10(Pval)")+
  theme_void()+
  theme(legend.position = "top",
        legend.key.size = unit(5,'mm'),
        legend.text = element_text(size=10))+
  guides(color=guide_colorbar(title.position = "top",
                              title.hjust = 0.5,
                              barwidth = 20))

p.top

library(patchwork)

p.top+
  p.bottom+
  plot_layout(ncol = 1,heights = c(1,5))