tests/test-HeatmapList-class.R

In ComplexHeatmap: Make Complex Heatmaps

library(circlize)
library(ComplexHeatmap)
library(GetoptLong)

set.seed(123)
nr1 = 10; nr2 = 8; nr3 = 6
nc1 = 6; nc2 = 8; nc3 = 10
mat1 = 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))
   )

rownames(mat1) = paste0("row_1_", seq_len(nrow(mat1)))
colnames(mat1) = paste0("column_1_", seq_len(nrow(mat1)))

nr3 = 10; nr1 = 8; nr2 = 6
nc3 = 6; nc1 = 8; nc2 = 10
mat2 = 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))
   )

rownames(mat2) = paste0("row_2_", seq_len(nrow(mat2)))
colnames(mat2) = paste0("column_2_", seq_len(nrow(mat2)))


ht_list = Heatmap(mat1) + Heatmap(mat2)
draw(ht_list)

######### legend ############
draw(ht_list, heatmap_legend_side = "bottom")
draw(ht_list, heatmap_legend_side = "left")
draw(ht_list, heatmap_legend_side = "top")


########## width #############
ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1) + Heatmap(mat2, width = unit(8, "cm"))
draw(ht_list)
ht_list = Heatmap(mat1, width = unit(12, "cm")) + Heatmap(mat2, width = unit(8, "cm"))
draw(ht_list)

ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1) + Heatmap(mat2, width = unit(6, "cm"))
draw(ht_list)
ht_list = Heatmap(mat1, width = unit(6, "cm")) + Heatmap(mat2, width = unit(6, "cm"))
draw(ht_list)
ht_list = Heatmap(mat1, width = 4) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1, width = 2) + Heatmap(mat2, width = 1)
draw(ht_list)


########### height ###########
ht_list = Heatmap(mat1, height = unit(6, "cm")) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1, heatmap_height = unit(6, "cm")) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1, width = unit(6, "cm"), height = unit(6, "cm")) + 
	Heatmap(mat2, width = unit(6, "cm"), height = unit(6, "cm"))
draw(ht_list, column_title = "foooooooooo", row_title = "baaaaaaaaaaar")

##### split #####
ht_list = Heatmap(mat1, name = "m1", row_km = 2) + Heatmap(mat2, name = "m2", row_km = 3)
draw(ht_list, main_heatmap = "m1")
draw(ht_list, main_heatmap = "m2")

ht_list = Heatmap(mat1, name = "m1", row_km = 2, column_km = 3, width = unit(8, "cm"), height = unit(6, "cm")) + 
	Heatmap(mat2, name = "m2", row_km = 3, column_km = 2, width = unit(8, "cm"), height = unit(10, "cm"))
draw(ht_list, main_heatmap = "m1", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")
draw(ht_list, main_heatmap = "m2", column_title = "foooooooooo", row_title = "baaaaaaaaaaar")

##### adjust column annotations #####
ha1 = HeatmapAnnotation(foo = 1:24, bar = anno_points(24:1, height = unit(4, "cm")))
ha2 = HeatmapAnnotation(bar = anno_points(24:1), foo = 1:24)
ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
draw(ht_list)
ha2 = HeatmapAnnotation(foo = 1:24)
ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2, top_annotation = ha2)
draw(ht_list)
ht_list = Heatmap(mat1, top_annotation = ha1) + Heatmap(mat2)
draw(ht_list)
ht_list = Heatmap(mat1, bottom_annotation = ha1) + Heatmap(mat2)
draw(ht_list)


#### row annotations #####
ha = rowAnnotation(foo = 1:24, bar = anno_points(24:1), width = unit(6, "cm"))
ht_list = Heatmap(mat1) + ha
draw(ht_list)
ht_list = Heatmap(mat1, width = unit(6, "cm")) + ha
draw(ht_list)
ht_list = Heatmap(mat1, width = unit(6, "cm"), row_km = 2) + ha
draw(ht_list)

ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") +
  rowAnnotation(foo = 1:10, bar = anno_points(10:1)) + 
  Heatmap(matrix(runif(100), 10), name = "runif")
summary(ht_list[1:5, ])
summary(ht_list[1:5, 1])
summary(ht_list[1:5, "rnorm"])
summary(ht_list[1:5, c("rnorm", "foo")])

ht_list = Heatmap(matrix(rnorm(100), 10), name = "rnorm") %v%
  columnAnnotation(foo = 1:10, bar = anno_points(10:1)) %v%
  Heatmap(matrix(runif(100), 10), name = "runif")
summary(ht_list[, 1:5])
summary(ht_list[1, 1:5])
summary(ht_list["rnorm", 1:5])
summary(ht_list[c("rnorm", "foo"), 1:5])