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library(circlize)
library(ComplexHeatmap)
library(GetoptLong)
ha = HeatmapAnnotation(foo = 1:10)
ha
ha = HeatmapAnnotation(foo = cbind(1:10, 10:1))
ha
draw(ha, test = "matrix as column annotation")
ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
pt = anno_points(1:10), annotation_name_side = "left")
draw(ha, test = "complex annotations")
ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
pt = anno_points(1:10), annotation_name_side = "left", height = unit(8, "cm"))
draw(ha, test = "complex annotations")
ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE))
ha = HeatmapAnnotation(foo = 1:10,
bar = cbind(1:10, 10:1),
pt = anno_points(1:10),
gap = unit(2, "mm"))
draw(ha, test = "complex annotations")
ha2 = re_size(ha, annotation_height = unit(1:3, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, annotation_height = 1, height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, annotation_height = 1:3, height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, annotation_height = unit(c(1, 2, 3), c("null", "null", "cm")), height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, annotation_height = unit(c(2, 2, 3), c("cm", "null", "cm")), height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, annotation_height = unit(c(2, 2, 3), c("cm", "cm", "cm")))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha[, 1:2], annotation_height = 1, height = unit(4, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha[, 1:2], annotation_height = c(1, 4), height = unit(4, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha[, 1:2], height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
ha2 = re_size(ha, height = unit(6, "cm"))
draw(ha2, test = "complex annotations")
#### test anno_empty and self-defined anotation function
ha = HeatmapAnnotation(foo = anno_empty(), height = unit(4, "cm"))
draw(ha, 1:10, test = "anno_empty")
ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))
draw(ha, 1:10, test = "anno_empty")
ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))
draw(ha, 1:10, test = "anno_empty")
ha = HeatmapAnnotation(foo = function(index) {grid.rect()}, bar = 1:10, height = unit(4, "cm"))
draw(ha, 1:10, test = "self-defined function")
lt = lapply(1:10, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
ha = HeatmapAnnotation(foo = 1:10, bar = sample(c("a", "b"), 10, replace = TRUE),
anno = anno_horizon(lt), which = "row")
draw(ha, test = "complex annotations on row")
## test row annotation with no heatmap
rowAnnotation(foo = 1:10, bar = anno_points(10:1))
if(0) {
HeatmapAnnotation(1:10)
HeatmapAnnotation(data.frame(1:10))
}
ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm")))
v = sample(letters[1:2], 50, replace = TRUE)
split = sample(letters[1:2], 50, replace = TRUE)
ht = Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)
draw(ht)
ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm")))
v = rnorm(50)
ht = Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)
draw(ht)
### auto adjust
m = matrix(rnorm(100), 10)
ht_list = Heatmap(m, top_annotation = HeatmapAnnotation(foo = 1:10), column_dend_height = unit(4, "cm")) +
Heatmap(m, top_annotation = HeatmapAnnotation(bar = anno_points(1:10)),
cluster_columns = FALSE)
draw(ht_list)
fun = function(index) {
grid.rect()
}
ha = HeatmapAnnotation(fun = fun, height = unit(4, "cm"))
draw(ha, 1:10, test = TRUE)
ha = rowAnnotation(fun = fun, width = unit(4, "cm"))
draw(ha, 1:10, test = TRUE)
## test anno_mark
m = matrix(rnorm(1000), nrow = 100)
ha1 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1)
draw(ht)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE) + ha1
draw(ht)
split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha1, row_split = split, gap = unit(1, "cm"))
draw(ht)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha1
draw(ht)
# ha has two annotations
ha2 = rowAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2)
draw(ht)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE) + ha2
draw(ht)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, right_annotation = ha2, row_split = split, gap = unit(1, "cm"))
draw(ht)
ht = Heatmap(m, name = "mat", cluster_rows = FALSE, row_split = split, gap = unit(1, "cm")) + ha2
draw(ht)
## test anno_mark as column annotation
m = matrix(rnorm(1000), ncol = 100)
ha1 = columnAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]))
ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1)
draw(ht)
ht_list = ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)
draw(ht_list)
split = rep("a", 100); split[c(1:4, 20, 60, 98:100)] = "b"
ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha1, column_split = split, column_gap = unit(1, "cm"))
draw(ht)
ht_list = ha1 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, gap = unit(1, "cm"))
draw(ht_list)
# ha has two annotations
ha2 = HeatmapAnnotation(foo = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10]), bar = 1:100)
ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2)
draw(ht)
ht_list = ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE)
draw(ht_list)
ht = Heatmap(m, name = "mat", cluster_columns = FALSE, top_annotation = ha2, column_split = split, column_gap = unit(1, "cm"))
draw(ht)
ht_list = ha2 %v% Heatmap(m, name = "mat", cluster_columns = FALSE, column_split = split, column_gap = unit(1, "cm"))
draw(ht_list)
### when there are only simple annotations
col_fun = colorRamp2(c(0, 10), c("white", "blue"))
ha = HeatmapAnnotation(
foo = cbind(a = 1:10, b = 10:1),
bar = sample(letters[1:3], 10, replace = TRUE),
col = list(foo = col_fun,
bar = c("a" = "red", "b" = "green", "c" = "blue")
),
simple_anno_size = unit(1, "cm")
)
draw(ha, test = TRUE)
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)
ind = sample(12, 12)
mat1 = mat1[ind, ]
mat2 = mat2[ind, ]
ha1 = HeatmapAnnotation(foo1 = 1:10,
annotation_height = unit(1, "cm"),
simple_anno_size_adjust = TRUE,
annotation_name_side = "left")
ha2 = HeatmapAnnotation(df = data.frame(foo1 = 1:10,
foo2 = 1:10,
foo4 = 1:10,
foo5 = 1:10))
ht1 = Heatmap(mat1, name = "rnorm", top_annotation = ha1)
ht2 = Heatmap(mat2, name = "runif", top_annotation = ha2)
draw(ht1 + ht2)
##### test size of a single simple annotation
ha = HeatmapAnnotation(foo1 = 1:10,
simple_anno_size = unit(1, "cm")
)
ha = HeatmapAnnotation(foo1 = 1:10,
annotation_height = unit(1, "cm"),
simple_anno_size_adjust = TRUE
)
ha = HeatmapAnnotation(foo1 = 1:10,
height = unit(1, "cm"),
simple_anno_size_adjust = TRUE
)
## annotation with the same names
set.seed(123)
m = matrix(rnorm(100), 10)
ha1 = HeatmapAnnotation(foo = sample(c("a", "b"), 10, replace = TRUE))
ha2 = HeatmapAnnotation(foo = sample(c("b", "c"), 10, replace = TRUE))
ht_list = Heatmap(m, top_annotation = ha1) +
Heatmap(m, top_annotation = ha2)
draw(ht_list)
ha1 = HeatmapAnnotation(foo = sample(c("a", "b"), 10, replace = TRUE),
annotation_legend_param = list(
foo = list(title = "letters",
at = c("a", "b", "c"),
labels = c("A", "B", "C")
)
))
ha2 = HeatmapAnnotation(foo = sample(c("b", "c"), 10, replace = TRUE))
ht_list = Heatmap(m, top_annotation = ha1) +
Heatmap(m, top_annotation = ha2)
draw(ht_list)
x = matrix(rnorm(6), ncol=3)
subtype_col = c("Basal" = "purple","Her2" = "black","Normal" = "blue")
h1 <- HeatmapAnnotation("Subtype" = c("Basal","Her2", "Normal"),
col = list("Subtype" = subtype_col))
h2 <- HeatmapAnnotation("Subtype" = c("Normal","Normal", "Basal"),
col = list("Subtype" = subtype_col))
ht_list = Heatmap(x,top_annotation = h1) + Heatmap(x,top_annotation = h2)
draw(ht_list)
### test annotation_label
ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
annotation_label = c("anno1", "anno2"))
draw(ha, test = TRUE)
ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
annotation_label = list(foo = "anno1"))
draw(ha, test = TRUE)
ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
annotation_label = list(
foo = gt_render("foo", gp = gpar(box_fill = "red"))))
draw(ha, test = TRUE)
ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],
annotation_label = list(
foo = gt_render("foo", gp = gpar(box_fill = "red")),
bar = gt_render("bar", gp = gpar(box_fill = "blue"))))
draw(ha, test = TRUE)
### test whether arguments can be captured
HeatmapAnnotation(a = 1:10)
rowAnnotation(a = 1:10)
columnAnnotation(a = 1:10)
do.call(HeatmapAnnotation, list(a = 1:10))
do.call(rowAnnotation, list(a = 1:10))
do.call(columnAnnotation, list(a = 1:10))
do.call("HeatmapAnnotation", list(a = 1:10))
do.call("rowAnnotation", list(a = 1:10))
do.call("columnAnnotation", list(a = 1:10))
f = function() HeatmapAnnotation(a = 1:10)
f()
f = function() rowAnnotation(a = 1:10)
f()
f = function() columnAnnotation(a = 1:10)
f()
sapply(1, function(x) HeatmapAnnotation(a = 1:10))
sapply(1, function(x) rowAnnotation(a = 1:10))
sapply(1, function(x) columnAnnotation(a = 1:10))
mapply(function(x, y) HeatmapAnnotation(a = 1:10), list(1), list(1))
mapply(function(x, y) rowAnnotation(a = 1:10), list(1), list(1))
mapply(function(x, y) columnAnnotation(a = 1:10), list(1), list(1))
try({
HeatmapAnnotation(1:10)
HeatmapAnnotation(df = data.frame(a = 1:10), a = 1:10)
})
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