I'm trying to create a list of heatmaps with added elements to the plot. The code I'm using is derived from the complex heatmap tutorial: https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html
Here is a simplified version of my function:
library(ComplexHeatmap)
library(GetoptLong) # for the function qq()
make_heatmap <-
function(seed) {
set.seed(seed)
mat2 = matrix(rnorm(50 * 50), nrow = 50)
split = rep(1:5, each = 10)
ha = HeatmapAnnotation(
empty = anno_empty(border = FALSE, height = unit(8, "mm")),
foo = anno_block(gp = gpar(fill = 2:6), labels = LETTERS[1:5])
)
group_block_anno = function(group,
empty_anno,
gp = gpar(),
label = NULL,
label_gp = gpar()) {
seekViewport(qq("annotation_@{empty_anno}_@{min(group)}"))
loc1 = deviceLoc(x = unit(0, "npc"), y = unit(0, "npc"))
seekViewport(qq("annotation_@{empty_anno}_@{max(group)}"))
loc2 = deviceLoc(x = unit(1, "npc"), y = unit(1, "npc"))
seekViewport("global")
grid.rect(
loc1$x,
loc1$y,
width = loc2$x - loc1$x,
height = loc2$y - loc1$y,
just = c("left", "bottom"),
gp = gp
)
if (!is.null(label)) {
grid.text(
label,
x = (loc1$x + loc2$x) * 0.5,
y = (loc1$y + loc2$y) * 0.5,
gp = label_gp
)
}
}
htmp <-
Heatmap(
mat2,
name = "mat2",
column_split = split,
top_annotation = ha,
column_title = NULL
)
print(htmp)
group_block_anno(1:3, "empty", gp = gpar(fill = "red"), label = "group 1")
group_block_anno(4:5, "empty", gp = gpar(fill = "blue"), label = "group 2")
}
Then, I want to save the plots with different parameters in a list using sapply:
heatmap.list <- sapply(c(1,10,100,1000), make_heatmap)
By calling heatmap.list[1] I would expect a heatmap like this:
However, my output for heatmap.list is the following:
heatmap.list
[,1] [,2] [,3] [,4]
label "group 2" "group 2" "group 2" "group 2"
x 6.86002 6.86002 6.86002 6.86002
y 5.88428 5.88428 5.88428 5.88428
just "centre" "centre" "centre" "centre"
hjust NULL NULL NULL NULL
vjust NULL NULL NULL NULL
rot 0 0 0 0
check.overlap FALSE FALSE FALSE FALSE
name "GRID.text.33404" "GRID.text.33501" "GRID.text.33598" "GRID.text.33695"
gp List,0 List,0 List,0 List,0
vp NULL NULL NULL NULL
I tried using recordPlot() at the end of my function,
make_heatmap <-
function(seed) {
#same as before
.
.
.
print(htmp)
group_block_anno(1:3, "empty", gp = gpar(fill = "red"), label = "group 1")
group_block_anno(4:5, "empty", gp = gpar(fill = "blue"), label = "group 2")
record.htmp <- recordPlot()
plot.new()
record.htmp
}
heatmap.list <- sapply(c(1, 10, 100, 1000), make_heatmap)
But the output is as follows:
heatmap.list
[,1] [,2] [,3] [,4]
[1,] List,502 List,502 List,502 List,502
[2,] Raw,35992 Raw,35992 Raw,35992 Raw,35992
[3,] List,2 List,2 List,2 List,2
Is there a way to get my desired heatmap list? I have searched a lot, but I couldn't find a solution.
EDIT Solution:
As Robert Hacken suggested, using lapply() instead of sapply() solves the problem. I posted the corrected function here for possibly similar problems:
library(ComplexHeatmap)
library(GetoptLong) # for the function qq()
make_heatmap <-
function(seed) {
set.seed(seed)
mat2 = matrix(rnorm(50 * 50), nrow = 50)
split = rep(1:5, each = 10)
ha = HeatmapAnnotation(
empty = anno_empty(border = FALSE, height = unit(8, "mm")),
foo = anno_block(gp = gpar(fill = 2:6), labels = LETTERS[1:5])
)
group_block_anno = function(group,
empty_anno,
gp = gpar(),
label = NULL,
label_gp = gpar()) {
seekViewport(qq("annotation_@{empty_anno}_@{min(group)}"))
loc1 = deviceLoc(x = unit(0, "npc"), y = unit(0, "npc"))
seekViewport(qq("annotation_@{empty_anno}_@{max(group)}"))
loc2 = deviceLoc(x = unit(1, "npc"), y = unit(1, "npc"))
seekViewport("global")
grid.rect(
loc1$x,
loc1$y,
width = loc2$x - loc1$x,
height = loc2$y - loc1$y,
just = c("left", "bottom"),
gp = gp
)
if (!is.null(label)) {
grid.text(
label,
x = (loc1$x + loc2$x) * 0.5,
y = (loc1$y + loc2$y) * 0.5,
gp = label_gp
)
}
}
htmp <-
Heatmap(
mat2,
name = "mat2",
column_split = split,
top_annotation = ha,
column_title = NULL
)
print(htmp)
group_block_anno(1:3, "empty", gp = gpar(fill = "red"), label = "group 1")
group_block_anno(4:5, "empty", gp = gpar(fill = "blue"), label = "group 2")
record.htmp <- recordPlot()
plot.new()
record.htmp
}
heatmap.list <- lapply(c(1, 10, 100, 1000), make_heatmap)
EDIT 2:
heatmap.list <- sapply(c(1, 10, 100, 1000), make_heatmap, simplify = F)
Works aswell, which allows to access the elements of the list by name with heatmap.list$parameter, which might improve the workflow.
You can use lapply instead of sapply so that the result is not simplified into a matrix and then get e.g. the first element with heatmap.list[[1]].