Upset 图

注记

Hiplot 网站

本页面为 Hiplot Upset Plot 插件的源码版本教程，您也可以使用 Hiplot 网站实现无代码绘图，更多信息请查看以下链接:

https://hiplot.cn/basic/upset-plot?lang=zh_cn

Upset 可用于展示集合之间的交互关系。

环境配置

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

• 编程语言: R

• 依赖包: VennDiagram; ComplexHeatmap; ggplotify; ggplot2

# 安装包
if (!requireNamespace("VennDiagram", quietly = TRUE)) {
  install.packages("VennDiagram")
}
if (!requireNamespace("ComplexHeatmap", quietly = TRUE)) {
  install_github("jokergoo/ComplexHeatmap")
}
if (!requireNamespace("ggplotify", quietly = TRUE)) {
  install.packages("ggplotify")
}
if (!requireNamespace("ggplot2", quietly = TRUE)) {
  install.packages("ggplot2")
}

# 加载包
library(VennDiagram)
library(ComplexHeatmap)
library(ggplotify)
library(ggplot2)

数据准备

数据表可输入两种类型：list 和 binary。其中 list 格式为每列为一个集合，并包含所有集合对应的元素。binary 格式第一列为全部集合的全部元素，后续列为 0 和 1 组成的数值矩阵，1 则表明对应行元素存在于某个集合，0 则表示不存在。

# 加载数据
data <- read.delim("files/Hiplot/177-upset-plot-data.txt", header = T)

# 整理数据格式
for (i in seq_len(ncol(data))) {
  data[is.na(data[, i]), i] <- ""
}
data2 <- as.list(data)
data2 <- lapply(data2, function(x) {x[x != ""]})
data2 <- list_to_matrix(data2)
m = make_comb_mat(data2, mode = "distinct")
ss = set_size(m)
cs = comb_size(m)
set_order <- order(ss)
comb_order <- order(comb_degree(m), -cs)

# 查看数据
head(data)

     Set1      Set2     Set3      Set4    Set5      Set6    Set7     Set8
1   ISG15      HES5     DVL1   MATP6P1 FAM132A   FAM132A FAM132A  TNFRSF4
2  TTLL10  AURKAIP1 ARHGEF16   MIR551A    AGRN   MIR551A WBP1LP6   WASH7P
3    HES4 LINC00982   OR4F16  C1orf222 WBP1LP6   MIR200B   PANK4   TMEM52
4  OR4G4P    FAM87B      SKI   MIR200B  KLHL17    ATAD3C  OR4G4P   MMP23B
5 MND2P28       SKI   WASH7P LINC00115  FAM41C   ANKRD65   SSU72   CDK11B
6  FAM87B     GABRD    MEGF6    ATAD3B   PANK4 LINC01128 MND2P28 C1orf170

可视化

# Upset 图
p <- as.ggplot(function(){
  top_annotation <- HeatmapAnnotation(
    Intersections = anno_barplot(
      cs, ylim = c(0, max(cs)*1.1), 
      border = FALSE, 
      gp = gpar(fill = "#000000", fontsize = 10), 
      height = unit(5, "cm")
    ), 
    annotation_name_side = "left", 
    annotation_name_rot = 90
  )
  
  left_annotation <- rowAnnotation(
    Numbers = anno_barplot(-ss, axis_param = list(
      at = seq(-max(ss), 0, round(max(ss)/5)),
      labels = rev(seq(0, max(ss), round(max(ss)/5))),
      labels_rot = 0),
      baseline = 0,
      border = FALSE, 
      gp = gpar(fill = "#000000", fontsize = 10), 
      width = unit(4, "cm")
    ),
    set_name = anno_text(set_name(m), location = 0.5,  just = "center",
                         width = max_text_width(set_name(m)) + unit(5, "mm"))
  )
  
  ht = UpSet(m, comb_col = "#000000", bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC",
             pt_size = unit(3, "mm"), lwd = 2, set_order = set_order,
             comb_order = comb_order, top_annotation = top_annotation,
             left_annotation = left_annotation,  right_annotation = NULL,
             show_row_names = FALSE)
  ht = draw(ht)
  od = column_order(ht)
  decorate_annotation("Intersections", {
    grid.text(cs[od], x = seq_along(cs), y = unit(cs[od], "native") + unit(2, "pt"),
              default.units = "native", just = c("left", "bottom"), 
              gp = gpar(fontsize = 10, col = "#000000",
              fontfamily = "Arial"), hjust = 0.5)
  })
})
p <- p + ggtitle("Upset Plot") + 
  theme(plot.title = element_text(hjust = 0.6))

p

图 1: Upset 图