从 pheatmap 中的 cutree_rows 组中拉出 genes/observations

Question

如何从 pheatmap 中的 cutree_rows = 3 生成的行组中提取 genes/observations？会是 obj$tree_row$...?

obj <- pheatmap(mat, annotation_col = anno, fontsize_row = 10, show_colnames = F, show_rownames = F, cutree_cols = 3, cluster_cols = FALSE, color = col, scale = 'row',cutree_rows = 3)

我看到如果你通过运行 obj$kmeans$cluster 应用 k 意味着你可以找到基因列表，就像这里 is there a way to preserve the clustering in a heatmap but reduce the number of observations?

Answer 1

你可以在上面再做cutree，比如数据是这样的：

set.seed(2020)
mat = matrix(rnorm(200),20,10)
rownames(mat) = paste0("g",1:20)
obj = pheatmap(mat,cluster_cols = FALSE, scale = 'row',cutree_rows = 3)

做 cutree :

cl = cutree(obj$tree_row,3)

ann = data.frame(cl)
rownames(ann) = rownames(mat)

ann
    cl
g1   1
g2   2
g3   1
g4   2
g5   3
g6   1
g7   2
g8   1
g9   1
g10  2
g11  3
g12  2
g13  2
g14  1
g15  2
g16  2
g17  1
g18  3
g19  3
g20  2

我们再次绘制它以确保它是正确的，

pheatmap(mat,cluster_cols = FALSE, scale = 'row',cutree_rows = 3,annotation_row=ann)

从 pheatmap 中的 cutree_rows 组中拉出 genes/observations

Pull out genes/observations from cutree_rows groups in pheatmap

r

heatmap

hierarchical-clustering

pheatmap

rna-seq