R/etc/linkedSegments.r

   1 #!/usr/bin/env littler
   2 # 三组或更多组的画法，只需添加数据即可
   3 # https://mp.weixin.qq.com/s/FZWinr14RTs6YSUE_juaug
   4 # Galaxy实测，两组也行。
   5
   6 library(tidyverse)
   7
   8 df <- data.frame(
   9   Phylum=c("Ruminococcaceae","Bacteroidaceae","Eubacteriaceae","Lachnospiraceae","Porphyromonadaceae"),
  10   GroupA=c(37.7397,31.34317,222.08827,5.08956,3.7393),
  11   GroupB=c(113.2191,94.02951,66.26481,15.26868,11.2179),
  12   GroupC=c(123.2191,94.02951,46.26481,35.26868,1.2179),
  13   GroupD=c(37.7397,31.34317,222.08827,5.08956,3.7393)
  14 )
  15
  16 df.long <- df %>% gather(group, abundance, -Phylum)
  17
  18 ## 组间连线数据：
  19 ## 假设第一列是Phylum
  20 link_dat <- df %>%
  21   arrange(by=desc(Phylum)) %>%
  22   mutate_if(is.numeric, cumsum)
  23 bar.width <- 0.7
  24 link_dat <- link_dat[, c(1,2,rep(3:(ncol(link_dat)-1),each=2), ncol(link_dat))]
  25 link_dat <- data.frame(y=t(matrix(t(link_dat[,-1]), nrow=2)))
  26 link_dat$x.1 <- 1:(ncol(df)-2)+bar.width/2
  27 link_dat$x.2 <- 1:(ncol(df)-2)+(1-bar.width/2)
  28
  29 p <- ggplot(df.long, aes(x=group, y=abundance, fill=Phylum)) +
  30      geom_bar(stat = "identity", width=bar.width, col='black') +
  31      geom_segment(data=link_dat, aes(x=x.1, xend=x.2, y=y.1, yend=y.2), inherit.aes = F)
  32
  33 pdf(file="linkedSegments.pdf")
  34 print(p)
  35 dev.off()