系统树图

作者

[编辑] 郑虎;

[审核] .

系统树图是一种以树的形状表示的图。这种图表在不同情景有不同的含义。如：在层次聚类中，说明了相应分析产生的聚类的排列。在生物信息中，它显示基因或样本的聚集，有时在热图的边缘。

环境配置

  • 系统: Cross-platform (Linux/MacOS/Windows)

  • 编程语言: R

  • 依赖包: ape; ggplotify

# 安装包
if (!requireNamespace("ape", quietly = TRUE)) {
  install.packages("ape")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}

# 加载包
library(ape)
library(ggplotify)

数据准备

# 加载数据
data <- read.delim("files/Hiplot/037-dendrogram-data.txt", header = T)

# 整理数据格式
data <- data[, -1]

# 查看数据
head(data)
        M1       M2        M3       M4       M5       M6       M7       M8
1 6.599344 5.226266  3.693288 3.938501 4.527193 9.308119 8.987865 7.658312
2 5.760380 4.892783  5.448924 3.485413 3.855669 8.662081 8.793320 8.765915
3 9.561905 4.549168  3.998655 5.614384 3.904793 9.790770 7.133188 7.379591
4 8.396409 8.717055  8.039064 7.643060 9.274649 4.417013 4.725270 3.542217
5 8.419766 8.268430  8.451181 9.200732 8.598207 4.590033 5.368268 4.136667
6 7.653074 5.780393 10.633550 5.913684 8.805605 5.890120 5.527945 3.822596
        M9      M10
1 8.666038 7.419708
2 8.097206 8.262942
3 7.938063 6.154118
4 4.305187 6.964710
5 4.910986 4.080363
6 4.041078 7.956589

可视化

# 系统树图
d <- dist(t(data), method = "euclidean")
hc <- hclust(d, method = "complete")
clus <- cutree(hc, 4)

p <- as.ggplot(function() {
  par(mar = c(5, 5, 10, 5), mgp = c(2.5, 1, 0))
  plot(as.phylo(hc),
       type = "phylogram",
       tip.color = c("#00468bff","#ed0000ff","#42b540ff","#0099b4ff")[clus], 
       label.offset = 1,
       cex = 1, font = 2, use.edge.length = T
       )
  title("Dendrogram Plot", line = 1)
  })

p
图 1: D3 词云