• 如果是畫簡單的熱圖可以用pheatmap，上手簡單，網(wǎng)上教程特別多，畫出來很好看（pheatmap缺點：legend位置不可改；colnames和rownames位置不可改，字體大小可改；可在最上面的位置加注釋，左右下不可加注釋，注釋形式只能是顏色，文本和圖形都不可以加；可以按行列加gap，便于看分組信息；可以在cell里顯示數(shù)值大小，數(shù)值可以控制小數(shù)點位數(shù)）

• 為什么要用complexheatmap？我們看看他強大的功能：

  
  
  圖片.png

如果你的圖需要：

• 行注釋,列注釋都有或者其一; 在heatmap四周注釋各種圖或者文本
• 畫了好幾個熱圖要拼起來（我試過cow_plot,ggarrange總是失敗，如果大家成功了可以教我）
• 圖例和注釋的圖例位置或者方向調(diào)整
  -畫分類型變量

complexheatmap用起來！

1.行列注釋：

這個柱子可以換成文本或者圖

ha = HeatmapAnnotation(df = df, which = "row", width = unit(1, "cm"))
ht1 = Heatmap(mat, name = "ht1")
ht1 + ha + ht1

圖片.png

ht1 = Heatmap(mat, name = "ht1", km = 2)
ha_boxplot = HeatmapAnnotation(boxplot = anno_boxplot(mat, which = "row"), 
    which = "row", width = unit(2, "cm"))
draw(ha_boxplot + ht1, row_hclust_side = "left", row_sub_title_side = "right")

圖片.png

ha_column1 = HeatmapAnnotation(points = anno_points(rnorm(10)))
ht1 = Heatmap(mat, name = "ht1", km = 2, row_title = "Heatmap 1", column_title = "Heatmap 1", 
   top_annotation = ha_column1)

ha_column2 = HeatmapAnnotation(df = data.frame(type = c(rep("a", 5), rep("b", 5))))
ht2 = Heatmap(mat, name = "ht2", row_title = "Heatmap 2", column_title = "Heatmap 2",
   bottom_annotation = ha_column2)

ht_list = ht1 + ht2
draw(ht_list, row_title = "Heatmap list", column_title = "Heatmap list", 
   heatmap_legend_side = "right", annotation_legend_side = "left")

圖片.png

2.把多個heatmap拼起來，還可以自己調(diào)圖之間的間距，圖的大小

ha = HeatmapAnnotation(points = anno_points(rnorm(10)))
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", top_annotation = ha, show_heatmap_legend = FALSE)
lgd = legendGrob(c("dots"), pch = 16)
draw(ht1 + ht2, annotation_legend_list = list(lgd))

圖片.png

調(diào)間距：

draw(ht_list + ht_list, gap = unit(c(3, 6, 9, 0), "mm"))

圖片.png

調(diào)大小

ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1")
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2", width = unit(5, "cm"))
ht1 + ht2

圖片.png

3.圖例方向調(diào)整

df = data.frame(type = c(rep("a", 5), rep("b", 5)))
ha = HeatmapAnnotation(df = df, col = list(type = c("a" =  "red", "b" = "blue")))

ht1 = Heatmap(mat, name = "ht1", column_title = "Heatmap 1", top_annotation = ha)
ht2 = Heatmap(mat, name = "ht2", column_title = "Heatmap 2")
ht_list = ht1 + ht2

draw(ht_list)

圖片.png

draw(ht_list, heatmap_legend_side = "left", annotation_legend_side = "bottom")

圖片.png