1.1 General design
A single heatmap is composed of the heatmap body and the heatmap components. The heatmap body can be split by rows and columns. The heatmap components are titles, dendrograms, matrix names and heatmap annotations, which are put on the four sides of the heamap body. The heatmap components are reordered or split according to the heatmap body. |
3 Heatmap Annotations
A simple usage of heatmap annotations
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)
Color of annotations
library(circlize)
col_fun = colorRamp2(c(0, 5, 10), c("blue", "white", "red"))
ha = HeatmapAnnotation(foo = 1:10, col = list(foo = col_fun))
ha = HeatmapAnnotation(bar = sample(letters[1:3], 10, replace = TRUE),
col = list(bar = c("a" = "red", "b" = "green", "c" = "blue")))
specify more than one vectors
ha = HeatmapAnnotation(
foo = 1:10,
bar = sample(letters[1:3], 10, replace = TRUE),
col = list(foo = col_fun,
bar = c("a" = "red", "b" = "green", "c" = "blue")))
annotation table by df
anno_df = data.frame(foo = 1:10,
bar = sample(letters[1:3], 10, replace = TRUE))
ha = HeatmapAnnotation(df = anno_df,
col = list(foo = col_fun,
bar = c("a" = "red", "b" = "green", "c" = "blue")))
anno_simple() makes heatmap-like annotations
ha = HeatmapAnnotation(foo = anno_simple(1:10, pch = 1,
pt_gp = gpar(col = "red"), pt_size = unit(1:10, "mm")))
3.4 Block annotation
Heatmap(matrix(rnorm(100), 10), name = "mat",
top_annotation = HeatmapAnnotation(foo = anno_block(gp = gpar(fill = 2:4))),
column_km = 3)
** other annotation graphics
ha = HeatmapAnnotation(foo = anno_points(runif(10))) #3.6 Points annotation**
ha = HeatmapAnnotation(foo = anno_lines(runif(10))) #3.7 Lines annotation
ha = HeatmapAnnotation(foo = anno_barplot(1:10)) #3.8 Barplot annotation
## a barplot annotation which visualizes a proportion matrix
m = matrix(runif(4*10), nc = 4)
m = t(apply(m, 1, function(x) x/sum(x)))
ha = HeatmapAnnotation(foo = anno_barplot(m, gp = gpar(fill = 2:5),
bar_width = 1, height = unit(6, "cm")))
ha = HeatmapAnnotation(foo = anno_boxplot(m, height = unit(4, "cm"))) #3.9 Boxplot annotation
ha = rowAnnotation(foo = anno_histogram(m)) # apply m
on rows #3.10 Histogram annotation
3.18 Multiple annotations
ha = HeatmapAnnotation(foo = 1:10,
bar = cbind(1:10, 10:1),
pt = anno_points(1:10),
show_legend = c("bar" = FALSE))
Heatmap(matrix(rnorm(100), 10), name = "mat", top_annotation = ha) |
4 A List of Heatmaps
The main feature of ComplexHeatmap package is it supports to concatenate a list of heatmaps and annotations horizontally or vertically so that it makes it possible to visualize the associations from various sources of information.
concatenate heatmaps
ht1 = Heatmap(mat1, name = "rnorm")
ht2 = Heatmap(mat2, name = "runif")
ht3 = Heatmap(le, name = "letters")
ht1 + ht2 + ht3
4.1 Titles
draw(ht_list, row_title = "Three heatmaps, row title", row_title_gp = gpar(col = "red"),
column_title = "Three heatmaps, column title", column_title_gp = gpar(fontsize = 16))
4.3 Gap between heatmaps
draw(ht_list, ht_gap = unit(1, "cm"))
4.8 Concatenate only the annotations
rowAnnotation(foo = 1:12) +
rowAnnotation(bar = anno_barplot(1:12, width = unit(4, "cm")))
4.9 Vertical concatenation
ht_list = ht1 %v% ht2 %v% ht3; draw(ht_list) |
2 A Single Heatmap
2.1 Colors
## continueous
library(circlize)
col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red"), space = "RGB")
Heatmap(mat, name = "mat", col = col_fun)
## discrete
discrete_mat = matrix(sample(1:4, 100, replace = TRUE), 10, 10)
colors = structure(1:4, names = c("1", "2", "3", "4")) # black, red, green, blue
Heatmap(discrete_mat, name = "mat", col = colors)
2.4 Set row and column orders
Heatmap(mat, name = "mat", row_order = order(as.numeric(gsub("row", "", rownames(mat)))),
column_order = order(as.numeric(gsub("column", "", colnames(mat)))))
2.7 Split by categorical variables
## split by a vector
Heatmap(mat, name = "mat",
row_split = rep(c("A", "B"), 9), column_split = rep(c("C", "D"), 12))
## split by a data frame
Heatmap(mat, name = "mat",
row_split = data.frame(rep(c("A", "B"), 9), rep(c("C", "D"), each = 9)))
## Order of slices
Heatmap(mat, name = "mat",
row_split = factor(rep(LETTERS[1:3], 6), levels = LETTERS[3:1]),
column_split = factor(rep(letters[1:6], 4), levels = letters[6:1]),
cluster_row_slices = FALSE,
cluster_column_slices = FALSE)
2.12 Get orders and dendrograms
small_mat = mat[1:9, 1:9]; ht1 = Heatmap(small_mat); row_order(ht1)
2.13 Subset a heatmap
ht = Heatmap(mat, name = "mat")
dim(ht); ht[1:10, 1:10] |
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7 OncoPrint
## If the separators are in ;:,|, oncoPrint() automatically spit the alteration strings##
get_type_fun = function(x) strsplit(x, ";")[[1]]
layer by layer style by specifying alter_fun as a list
col = c(snv = "red", indel = "blue")
oncoPrint(mat,
alter_fun = list(
snv = function(x, y, w, h) grid.rect(x, y, w0.9, h0.9,
gp = gpar(fill = col["snv"], col = NA)),
indel = function(x, y, w, h) grid.rect(x, y, w0.9, h0.4,
gp = gpar(fill = col["indel"], col = NA))), col = col)
7.1.2 grid-by-grid style by specifying alter_fun as a single function
oncoPrint(mat,
alter_fun = function(x, y, w, h, v) {
if(v["snv"]) grid.rect(x, y, w0.9, h0.9, # v["snv"] is a logical value
gp = gpar(fill = col["snv"], col = NA))
if(v["indel"]) grid.rect(x, y, w0.9, h0.4, # v["indel"] is a logical value
gp = gpar(fill = col["indel"], col = NA)) }, col = col)
7.1.3 Background
If alter_fun is specified as a list, the order of the elements controls the order of adding graphics. There is a special element called background which defines how to draw background and it should be always put as the first element in the alter_fun list.
7.2 Apply to cBioPortal dataset
col = c("HOMDEL" = "blue", "AMP" = "red", "MUT" = "#008000")
alter_fun = list(
background = function(x, y, w, h) {
grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"),
gp = gpar(fill = "#CCCCCC", col = NA)) },
HOMDEL = function(x, y, w, h) {
grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"),
gp = gpar(fill = col["HOMDEL"], col = NA)) },
AMP = function(x, y, w, h) {
grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"),
gp = gpar(fill = col["AMP"], col = NA))},
MUT = function(x, y, w, h) {
grid.rect(x, y, w-unit(0.5, "mm"), h*0.33,
gp = gpar(fill = col["MUT"], col = NA)) })
7.2.1 Remove empty rows and columns
oncoPrint(mat,
alter_fun = alter_fun, col = col,
remove_empty_columns = TRUE, remove_empty_rows = TRUE,
column_title = column_title, heatmap_legend_param = heatmap_legend_param)
7.2.2 Reorder the oncoPrint
sample_order = scan(paste0(system.file("extdata", package = "ComplexHeatmap"),
"/sample_order.txt"), what = "character")
oncoPrint(mat,
alter_fun = alter_fun, col = col,
row_order = 1:nrow(mat), column_order = sample_order,
remove_empty_columns = TRUE, remove_empty_rows = TRUE,
column_title = column_title, heatmap_legend_param = heatmap_legend_param)
7.2.3 OncoPrint annotations
oncoPrint(mat,
alter_fun = alter_fun, col = col,
top_annotation = HeatmapAnnotation(
column_barplot = anno_oncoprint_barplot("MUT", border = TRUE, # only MUT
height = unit(4, "cm"))),
right_annotation = rowAnnotation(
row_barplot = anno_oncoprint_barplot(c("AMP", "HOMDEL"), # only AMP and HOMDEL
border = TRUE, height = unit(4, "cm"),
axis_param = list(side = "bottom", labels_rot = 90))),
remove_empty_columns = TRUE, remove_empty_rows = TRUE,
column_title = column_title, heatmap_legend_param = heatmap_legend_param)
add more annotations in HeatmapAnnotation() or rowAnnotation()
oncoPrint(mat,
alter_fun = alter_fun, col = col,
remove_empty_columns = TRUE, remove_empty_rows = TRUE,
top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot(),
foo1 = 1:172,
bar1 = anno_points(1:172)),
left_annotation = rowAnnotation(foo2 = 1:26),
right_annotation = rowAnnotation(bar2 = anno_barplot(1:26)),
column_title = column_title, heatmap_legend_param = heatmap_legend_param)
split the heatmap list
ht_list = oncoPrint(mat,
alter_fun = alter_fun, col = col,
column_title = column_title, heatmap_legend_param = heatmap_legend_param) +
Heatmap(matrix(rnorm(nrow(mat)*10), ncol = 10), name = "expr", width = unit(4, "cm"))
draw(ht_list, row_split = sample(c("a", "b"), nrow(mat), replace = TRUE))
Get the subset of rows and columns
rownames(ht@matrix); colnames(ht@matrix) |
5 Legends
5.1 Continuous legends
library(circlize)
col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
lgd = Legend(col_fun = col_fun, title = "foo")
5.2 Discrete legends
lgd = Legend(labels = month.name[1:6], title = "foo", legend_gp = gpar(fill = 1:6))
5.4 Heatmap legends
m = matrix(rnorm(100), 10)
Heatmap(m, name = "mat", heatmap_legend_param = list(
at = c(-2, 0, 2),labels = c("low", "zero", "high"),
title = "Some values",legend_height = unit(4, "cm"),
title_position = "lefttop-rot"
))
5.4 annotation legends
ha = HeatmapAnnotation(foo = runif(10), bar = sample(c("f", "m"), 10, replace = TRUE),
annotation_legend_param = list(
foo = list(title = "Fooooooh",at = c(0, 0.5, 1), labels = c("zero", "median", "one") ),
bar = list( title = "Baaaaaaar",at = c("f", "m"),labels = c("Female", "Male"))))
Heatmap(m, name = "mat", top_annotation = ha)
5.6 The side of legends
draw(ht_list, heatmap_legend_side = "left", annotation_legend_side = "bottom") |
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