ComplexHeatmap provides general solutions of complex heatmap visualizaiton.

Basic

Example

First generate a random matrix.

set.seed(123)
nr1 = 4; nr2 = 8; nr3 = 6; nr = nr1 + nr2 + nr3
nc1 = 6; nc2 = 8; nc3 = 10; nc = nc1 + nc2 + nc3
mat = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1,   sd = 0.5), nr = nr1),
          matrix(rnorm(nr2*nc1, mean = 0,   sd = 0.5), nr = nr2),
          matrix(rnorm(nr3*nc1, mean = 0,   sd = 0.5), nr = nr3)),
    rbind(matrix(rnorm(nr1*nc2, mean = 0,   sd = 0.5), nr = nr1),
          matrix(rnorm(nr2*nc2, mean = 1,   sd = 0.5), nr = nr2),
          matrix(rnorm(nr3*nc2, mean = 0,   sd = 0.5), nr = nr3)),
    rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
          matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
          matrix(rnorm(nr3*nc3, mean = 1,   sd = 0.5), nr = nr3))
   )
mat = mat[sample(nr, nr), sample(nc, nc)] # random shuffle rows and columns
rownames(mat) = paste0("row", seq_len(nr))
colnames(mat) = paste0("column", seq_len(nc))

Make the corresponding heatmap.

library(ComplexHeatmap)
Heatmap(mat)

Split rows and columns.

Heatmap(mat, name = "mat", 
    row_split = rep(c("A", "B"), 9), column_split = rep(c("C", "D"), 12))

Add heatmap annotations.

set.seed(123)
mat = matrix(rnorm(100), 10)
rownames(mat) = paste0("R", 1:10)
colnames(mat) = paste0("C", 1:10)
column_ha = HeatmapAnnotation(foo1 = runif(10), bar1 = anno_barplot(runif(10)))
row_ha = rowAnnotation(foo2 = runif(10), bar2 = anno_barplot(runif(10)))
Heatmap(mat, name = "mat", top_annotation = column_ha, right_annotation = row_ha)

Add multiple heatmaps.

set.seed(123)
mat1 = matrix(rnorm(80, 2), 8, 10)
mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
rownames(mat1) = paste0("R", 1:12)
colnames(mat1) = paste0("C", 1:10)

mat2 = matrix(runif(60, max = 3, min = 1), 6, 10)
mat2 = rbind(mat2, matrix(runif(60, max = 2, min = 0), 6, 10))
rownames(mat2) = paste0("R", 1:12)
colnames(mat2) = paste0("C", 1:10)

le = sample(letters[1:3], 12, replace = TRUE)
names(le) = paste0("R", 1:12)

ind = sample(12, 12)
mat1 = mat1[ind, ]
mat2 = mat2[ind, ]
le = le[ind]

ht1 = Heatmap(mat1, name = "rnorm")
ht2 = Heatmap(mat2, name = "runif")
ht3 = Heatmap(le, name = "letters")

ht1 + ht2 + ht3