ggplot2绘制冲积条形图

常见的堆砌条形图看腻了，试试冲积条形吧！！

rm(list=ls())
pacman::p_load(tidyverse,magrittr,reshape,RColorBrewer,ggalluvial)

computed_persent <- function(path) {
  data <- path %>%
    read.delim(check.names = FALSE, row.names = 1)
  data2 <- data %>%
    mutate(sum = rowSums(.), persent = sum / sum(sum) * 100, sum = NULL,) %>%
    rbind(filter(., persent < 1) %>% colSums()) %>%
    mutate(OTU_ID = c(data %>% rownames(), "others"))
  filter(data2[1:(nrow(data2) - 1),], persent > 1) %>%
    rbind(data2[nrow(data2),]) %>%
    set_rownames(seq_len(nrow(.))) %>%
    return()
}
path <- "genus.xls" #此处写入的是文件路径
a1 <- computed_persent(path) %>% melt() %>% filter(variable !="persent")

colors <-c("#E41A1C","#1E90FF","#FF8C00","#4DAF4A","#984EA3",
           "#40E0D0","#FFC0CB","#00BFFF","#FFDEAD","#90EE90",
           "#EE82EE","#00FFFF","#F0A3FF", "#0075DC", 
           "#993F00","#4C005C","#2BCE48","#FFCC99",
           "#808080","#94FFB5","#8F7C00","#9DCC00",
           "#C20088","#003380","#FFA405","#FFA8BB",
           "#426600","#FF0010","#5EF1F2","#00998F",
           "#740AFF","#990000","#FFFF00")

a2 <- "group.txt" %>% read.delim()
a4 <- NULL

for (i in seq_len(nrow(a1))) { 
  a4[i] <- a2[which(a2[, 1] == a1[i, 2]), 2] }

a1[, 4] <- a4
#以上部分为数据过滤步骤
head(a1)
#------------------------------------------------------------------------------------
                      OTU_ID variable value V4
1                  Aeromonas       B1   144  B
2                Bacteroides       B1   282  B
3 Barnesiellaceae_uncultured       B1    34  B
4             Bradyrhizobium       B1   928  B
5              Brevundimonas       B1   414  B
6              Cetobacterium       B1   550  B
#----------------------------------------------------------------------------------
ggplot(a1,aes(variable,value,alluvium=OTU_ID,stratum = OTU_ID))+
  geom_alluvium(aes(fill = OTU_ID),alpha = .5,width = 0.6) + 
  geom_stratum(aes(fill = OTU_ID),width = 0.6)+
  facet_grid(. ~V4,scales = "free",space="free_x")+
  labs(x="",y="Proportions")+
  scale_fill_manual(values = colors)+labs(fill="")+
  theme(legend.title=element_blank())+
  scale_y_continuous(expand=c(0,0))+
  theme(panel.background = element_rect(fill='white',
                                  colour='black'))

bar.png
参考：http://corybrunson.github.io/ggalluvial/articles/ggalluvial.html
数据链接：https://pan.baidu.com/s/1HDVjd47YWN5_ayJCElGIpg
提取码: ejrr