R 数据可视化 —— 聚类热图 ComplexHeatmap装饰热图

前言

在绘制热图之后，仍会保留每个热图组件的绘图区域。因此，可以通过获取组件的绘图区域来添加或修改图形

可以使用 list_components() 获取热图的所有组件名称或 viewport 名称，例如

set.seed(123)
mat <- matrix(rnorm(80, 2), 8, 10)
mat <- rbind(mat, matrix(rnorm(40, -2), 4, 10))
rownames(mat) <- paste0("R", 1:12)
colnames(mat) <- paste0("C", 1:10)

ha_column1 <- HeatmapAnnotation(
  points = anno_points(rnorm(10)), 
  annotation_name_side = "left"
)
ht1 <- Heatmap(
  mat, name = "ht1", km = 2, 
  column_title = "Heatmap 1", 
  top_annotation = ha_column1, 
  row_names_side = "left"
)
ha_column2 <- HeatmapAnnotation(
  type = c(rep("a", 5), rep("b", 5)),
  col = list(type = c("a" = "red", "b" = "blue"))
)
ht2 <- Heatmap(
  mat, name = "ht2", row_title = "Heatmap 2", 
  column_title = "Heatmap 2",
  bottom_annotation = ha_column2, column_km = 2
)

ht_list <- ht1 + ht2 + 
  rowAnnotation(
    bar = anno_barplot(
      rowMeans(mat), width = unit(2, "cm"))
)
draw(
  ht_list, row_title = "Heatmap list", 
  column_title = "Heatmap list",
)

列出所有组件

> list_components()
 [1] "ROOT"                           "global"                         "global_layout"                 
 [4] "global-heatmaplist"             "main_heatmap_list"              "heatmap_ht1"                   
 [7] "ht1_heatmap_body_wrap"          "ht1_heatmap_body_1_1"           "ht1_heatmap_body_2_1"          
[10] "ht1_column_title_1"             "ht1_row_title_1"                "ht1_row_title_2"               
[13] "ht1_dend_row_1"                 "ht1_dend_row_2"                 "ht1_dend_column_1"             
[16] "ht1_row_names_1"                "ht1_row_names_2"                "ht1_column_names_1"            
[19] "annotation_points_1"            "heatmap_ht2"                    "ht2_heatmap_body_wrap"         
[22] "ht2_heatmap_body_1_1"           "ht2_heatmap_body_1_2"           "ht2_heatmap_body_2_1"          
[25] "ht2_heatmap_body_2_2"           "ht2_column_title_1"             "ht2_dend_column_1"             
[28] "ht2_dend_column_2"              "ht2_column_names_1"             "ht2_column_names_2"            
[31] "annotation_type_1"              "annotation_type_2"              "heatmap_heatmap_annotation_2"  
[34] "annotation_bar_1"               "annotation_bar_2"               "global-column_title_top"       
[37] "global_column_title"            "global-row_title_left"          "global_row_title"              
[40] "global-heatmap_legend_right"    "heatmap_legend"                 "global-annotation_legend_right"
[43] "annotation_legend"

1. 装饰函数

获取了所有组件的 viewport 名称之后，我们可以使用 seekViewport() 来获取对应的 viewport。

为了避免使用繁琐的 viewport 名称，ComplexHeatmap 包提供了 decorate_*() 形式的简便函数

decorate_heatmap_body()：装饰热图主体
decorate_annotation()：注释
decorate_dend()：树状图
decorate_title()：标题
decorate_dimnames()：行列名称
decorate_row_names()：行名，相当于 decorate_dimnames(..., which = "row")
decorate_column_names()：列名，相当于 decorate_dimnames(..., which = "column")
decorate_row_dend()：行树状图，相当于 decorate_dend(..., which = "row")
decorate_column_dend()：列树状图，相当于 decorate_dend(..., which = "column")
decorate_row_title()：行标题，相当于 decorate_title(..., which = "row")
decorate_column_title()：列标题，相当于 to decorate_title(..., which = "column")

这些函数需要传入热图或注释的名称、绘图块，如果热图分块了，需要设置分块索引

例如，对于下面的热图

ht_list <- draw(ht_list, row_title = "Heatmap list", column_title = "Heatmap list", 
               heatmap_legend_side = "right", annotation_legend_side = "left")

在第一个热图的第二个分块中，文本和线条注释

decorate_heatmap_body("ht1", {
  grid.text("outlier", 1.5/10, 2.5/4, default.units = "npc")
  grid.lines(
    c(0.5, 0.5), c(0, 1), 
    gp = gpar(lty = 2, lwd = 2, col = "green"))
}, slice = 2)

为第一个热图的树形图的不同类别添加不同的背景颜色

decorate_column_dend("ht1", {
  # 获取树状图
  tree = column_dend(ht_list)$ht1[[1]]
  # 将树状图分为两类
  ind = cutree(as.hclust(tree), k = 2)[order.dendrogram(tree)]
  # 获取每类的起始索引
  first_index = function(l) which(l)[1]
  # 获取没类的终止索引
  last_index = function(l) { x = which(l); x[length(x)] }
  x1 = c(first_index(ind == 1), first_index(ind == 2)) - 1
  x2 = c(last_index(ind == 1), last_index(ind == 2))
  # 为没类设置矩形背景色
  grid.rect(x = x1/length(ind), width = (x2 - x1)/length(ind), just = "left",
            default.units = "npc", gp = gpar(fill = c("#FF000040", "#00FF0040"), col = NA))
})

为第一个热图的第二个分块的行名，设置背景填充色

decorate_row_names("ht1", {
  grid.rect(gp = gpar(fill = "#FF000040"))
}, slice = 2)

为第一个热图的第一个分块的行标题设置背景填充色

decorate_row_title("ht1", {
  grid.rect(gp = gpar(fill = "#00FF0040"))
}, slice = 1)

在点图注释中添加一条水平线

decorate_annotation("points", {
  grid.lines(
    c(0, 1), unit(c(0, 0), "native"), 
    gp = gpar(col = "red"))
})