桑基图（SanKey）

SanKey plot

## 设置路劲
setwd("D:\\小杜的生信筆記\\桑基图")

## 导入R包
#BiocManager::install("ggalluvial")
library("ggplot2")
library("ggalluvial")

</pre>

</pre>

导入数据：

df <- read.table("SangKey_input.txt", header = T, row.names = 1, sep = '\t')
head(df)

数据格式:

> head(df)
   gene  lncRNA  miRNA
1 gene4 lncRNA1 miRNA2
2 gene4 lncRNA3 miRNA3
3 gene3 lncRNA5 miRNA3
4 gene2 lncRNA5 miRNA2
5 gene8 lncRNA4 miRNA1
6 gene8 lncRNA2 miRNA3

开始绘图:

定义颜色

mycol <- rep(c("#223D6C","#D20A13","#FFD121","#088247","#11AA4D","#58CDD9",
"#7A142C","#5D90BA","#029149","#431A3D","#91612D","#6E568C",
"#E0367A","#D8D155","#64495D","#7CC767"),2)

格式转换:

#格式转换
UCB_lodes <- to_lodes_form(df[,1:ncol(df)],
                           axes = 1:ncol(df),
                           id = "Cohort")

head(UCB_lodes)
Cohort x stratum
1 1 gene gene4
2 2 gene gene4
3 3 gene gene3
4 4 gene gene2
5 5 gene gene8
6 6 gene gene8

> tail(UCB_lodes)
    Cohort     x stratum
295     95 miRNA  miRNA4
296     96 miRNA  miRNA3
297     97 miRNA  miRNA3
298     98 miRNA  miRNA2
299     99 miRNA  miRNA3
300    100 miRNA  miRNA2

画图：

pdf("Sankey.pdf",width = 6, height = 6)
ggplot(UCB_lodes,
       aes(x = x, stratum = stratum, alluvium = Cohort,
           fill = stratum, label = stratum)) +
  scale_x_discrete(expand = c(0, 0)) + 
  geom_flow(width = 1/8) + #线跟方块间空隙的宽窄
  geom_stratum(alpha = .9,width = 1/10) + #方块的透明度、宽度
  geom_text(stat = "stratum", size = 3,color="black") + #文字大小、颜色

  #不喜欢默认的配色方案，用前面自己写的配色方案
  scale_fill_manual(values = mycol) +

  xlab("") + ylab("") +
  theme_bw() + #去除背景色
  theme(panel.grid =element_blank()) + #去除网格线
  theme(panel.border = element_blank()) + #去除外层边框
  theme(axis.line = element_blank(),axis.ticks = element_blank(),axis.text = element_blank()) + #去掉坐标轴
  ggtitle("")+
  guides(fill = FALSE) 
dev.off()

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ENDING !!!

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