ggplot2 -- 发散条形图/柱状偏差图 可视化差异通路

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# step 1
# 首先对上下调通路进行分组上色绘图放于坐标两侧

#### 发散条形图绘制 ####
library(tidyverse)  # ggplot2 stringer dplyr tidyr readr purrr  tibble forcats
library(ggthemes)
library(ggprism)

degs <- gsva_kegg_degs  #载入gsva的差异分析结果
Diff <- rbind(subset(degs,logFC>0)[1:20,], subset(degs,logFC<0)[1:20,]) #选择上下调前20通路     
dat_plot <- data.frame(id  = row.names(Diff),
                       p   = Diff$P.Value,
                       lgfc= Diff$logFC)
dat_plot$group <- ifelse(dat_plot$lgfc>0 ,1,-1)    # 将上调设为组1，下调设为组-1
dat_plot$lg_p <- -log10(dat_plot$p)*dat_plot$group # 将上调-log10p设置为正，下调-log10p设置为负

# 去掉多余文字
dat_plot$id[1:10]
dat_plot$id <- str_replace(dat_plot$id, "KEGG_","");dat_plot$id[1:10]

# 根据阈值分类
p_cutoff=0.001
dat_plot$threshold <- factor(ifelse(abs(dat_plot$p) <= p_cutoff,
                                   ifelse(dat_plot$lgfc >0 ,'Up','Down'),'Not'),
                            levels=c('Up','Down','Not'))
table(dat_plot$threshold)

# 根据p从小到大排序
dat_plot <- dat_plot %>% arrange(lg_p)
# id变成因子类型
dat_plot$id <- factor(dat_plot$id,levels = dat_plot$id)
# 绘制条形图
p <- ggplot(data = dat_plot,aes(x = id, y = lg_p, 
                                fill = threshold)) +
  geom_col()+
  coord_flip() + #坐标轴旋转
  scale_fill_manual(values = c('Up'= '#36638a','Not'='#cccccc','Down'='#7bcd7b')) +
  geom_hline(yintercept = c(-log10(p_cutoff),log10(p_cutoff)),color = 'white',size = 0.5,lty='dashed') +
  xlab('') + 
  ylab('-log10(P.Value) of GSVA score') + 了
  guides(fill="none")+ # 不显示图例
  theme_prism(border = T) +
  theme(
    plot.margin=unit(c(2,2,2,2),'lines'),#图片四周上右下左间距
    axis.text.y = element_blank(),
    axis.ticks.y = element_blank()
  )
p

# step 2
# 接着加上对应的分组标签

## 添加标签
# 小于-cutoff的数量
low1 <- dat_plot %>% filter(lg_p < log10(p_cutoff)) %>% nrow(); low1
# 小于0总数量
low0 <- dat_plot %>% filter(lg_p < 0) %>% nrow(); low0 
# 小于cutoff总数量
high0 <- dat_plot %>% filter(lg_p < -log10(p_cutoff)) %>% nrow(); high0 
# 总数量
high1 <- nrow(dat_plot); high1 

# 依次从下到上添加标签
p1 <- p + geom_text(data = dat_plot[1:low1,],aes(x = id,y = 0.1,label = id),
                   hjust = 0,color = 'black') + # 小于-cutoff的为黑色标签
  geom_text(data = dat_plot[(low1 +1):low0,],aes(x = id,y = 0.1,label = id),
            hjust = 0,color = 'grey') + # 灰色标签
  geom_text(data = dat_plot[(low0 + 1):high0,],aes(x = id,y = -0.1,label = id),
            hjust = 1,color = 'grey') + # 灰色标签
  geom_text(data = dat_plot[(high0 +1):high1,],aes(x = id,y = -0.1,label = id),
            hjust = 1,color = 'black') # 大于cutoff的为黑色标签
p1
ggsave("GSVA_barplot_pvalue.pdf",p1,width = 15,height  = 15)