# == title
# Make the Layout of a Single Heatmap
#
# == param
# -object A `Heatmap-class` object.
#
# == detail
# The layout of the single heatmap will be established by setting the size of each heatmap components.
# Also how to make graphics for heatmap components will be recorded by saving as functions.
#
# Whether to apply row clustering or column clustering affects the layout, so clustering should be applied
# first before making the layout.
#
# This function is only for internal use.
#
# == value
# A `Heatmap-class` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "make_layout",
signature = "Heatmap",
definition = function(object) {
if(object@layout$initialized) {
return(object)
}
# position of each row-slice
row_gap = object@matrix_param$row_gap
column_gap = object@matrix_param$column_gap
nr_slice = length(object@row_order_list)
nc_slice = length(object@column_order_list)
snr = sapply(object@row_order_list, length)
snc = sapply(object@column_order_list, length)
if(nr_slice == 1) {
slice_height = unit(1, "npc")
} else {
slice_height = (unit(1, "npc") - sum(row_gap[seq_len(nr_slice-1)]))*(snr/sum(snr))
}
for(i in seq_len(nr_slice)) {
if(i == 1) {
slice_y = unit(1, "npc")
} else {
slice_y = unit.c(slice_y, unit(1, "npc") - sum(slice_height[seq_len(i-1)]) - sum(row_gap[seq_len(i-1)]))
}
}
if(nc_slice == 1) {
slice_width = unit(1, "npc")
} else {
slice_width = (unit(1, "npc") - sum(column_gap[seq_len(nc_slice-1)]))*(snc/sum(snc))
}
for(i in seq_len(nc_slice)) {
if(i == 1) {
slice_x = unit(0, "npc")
} else {
slice_x = unit.c(slice_x, sum(slice_width[seq_len(i-1)]) + sum(column_gap[seq_len(i-1)]))
}
}
object@layout$slice = list(
x = slice_x,
y = slice_y,
width = slice_width,
height = slice_height,
just = c("left", "top")
)
if(length(object@matrix)) {
###########################################
## heatmap body
object@layout$layout_index = rbind(heatmapb_body = heatmap_layout_index("heatmap_body"))
object@layout$graphic_fun_list = list(function(object) {
for(i in seq_len(nr_slice)) {
for(j in seq_len(nc_slice)) {
draw_heatmap_body(object, kr = i, kc = j, x = slice_x[j], y = slice_y[i], width = slice_width[j], height = slice_height[i], just = c("left", "top"))
}
}
})
}
############################################
## title on top or bottom
column_title = object@column_title
column_title_side = object@column_title_param$side
column_title_gp = object@column_title_param$gp
column_title_rot = object@column_title_param$rot
if(length(column_title) > 0) {
if(column_title_side == "top") {
if(column_title_rot %in% c(0, 180)) {
object@layout$layout_size$column_title_top_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2
} else {
object@layout$layout_size$column_title_top_height = grobWidth(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2
}
object@layout$layout_index = rbind(object@layout$layout_index, column_title_top = heatmap_layout_index("column_title_top"))
} else {
if(column_title_rot %in% c(0, 180)) {
object@layout$layout_size$column_title_bottom_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2
} else {
object@layout$layout_size$column_title_bottom_height = grobWidth(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2
}
object@layout$layout_index = rbind(object@layout$layout_index, column_title_bottom = heatmap_layout_index("column_title_bottom"))
}
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
if(length(column_title) == 1 && nc_slice > 1) {
draw_title(object, k = 1, which = "column")
} else {
for(i in seq_len(nc_slice)) {
draw_title(object, k = i, which = "column", x = slice_x[i], width = slice_width[i], just = "left")
}
}
})
}
############################################
## title on left or right
row_title = object@row_title
row_title_side = object@row_title_param$side
row_title_gp = object@row_title_param$gp
row_title_rot = object@row_title_param$rot
if(length(row_title) > 0) {
if(row_title_side == "left") {
if(row_title_rot %in% c(0, 180)) {
object@layout$layout_size$row_title_left_width = max_text_width(row_title, gp = row_title_gp) + ht_opt$TITLE_PADDING*2
} else {
object@layout$layout_size$row_title_left_width = max_text_height(row_title, gp = row_title_gp) + ht_opt$TITLE_PADDING*2
}
object@layout$layout_index = rbind(object@layout$layout_index, row_title_left = heatmap_layout_index("row_title_left"))
} else {
if(row_title_rot %in% c(0, 180)) {
object@layout$layout_size$row_title_right_width = max_text_width(row_title, gp = row_title_gp) + ht_opt$TITLE_PADDING*2
} else {
object@layout$layout_size$row_title_right_width = max_text_height(row_title, gp = row_title_gp) + ht_opt$TITLE_PADDING*2
}
object@layout$layout_index = rbind(object@layout$layout_index, row_title_right = heatmap_layout_index("row_title_right"))
}
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
if(length(row_title) == 1 && nr_slice > 1) {
draw_title(object, k = 1, which = "row")
} else {
for(i in seq_len(nr_slice)) {
draw_title(object, k = i, which = "row", y = slice_y[i], height = slice_height[i], just = "top")
}
}
})
}
##########################################
## dend on left or right
show_row_dend = object@row_dend_param$show
row_dend_side = object@row_dend_param$side
row_dend_width = object@row_dend_param$width
row_dend_slice = object@row_dend_slice
if(show_row_dend) {
if(row_dend_side == "left") {
object@layout$layout_size$row_dend_left_width = row_dend_width
object@layout$layout_index = rbind(object@layout$layout_index, row_dend_left = heatmap_layout_index("row_dend_left"))
} else {
object@layout$layout_size$row_dend_right_width = row_dend_width
object@layout$layout_index = rbind(object@layout$layout_index, row_dend_right = heatmap_layout_index("row_dend_right"))
}
row_dend_max_height = dend_heights(row_dend_slice) + max(dend_heights(object@row_dend_list))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
if(row_dend_side == "left") {
pushViewport(viewport(x = unit(0, "npc"), width = unit(1, "npc") - ht_opt$DENDROGRAM_PADDING, just = "left"))
} else {
pushViewport(viewport(x = ht_opt$DENDROGRAM_PADDING, width = unit(1, "npc") - ht_opt$DENDROGRAM_PADDING, just = "left"))
}
for(i in seq_len(nr_slice)) {
draw_dend(object, k = i, which = "row", y = slice_y[i], height = slice_height[i], just = "top",
max_height = row_dend_max_height)
}
if(nr_slice > 1) {
if(row_dend_side == "left") {
pushViewport(viewport(xscale = c(0, row_dend_max_height)))
} else {
pushViewport(viewport(xscale = c(0, row_dend_max_height)))
}
p = sapply(object@row_dend_list, function(x) {
attr(x, "x")/nobs(x)
})
nb = sapply(object@row_dend_list, nobs)
slice_leaf_pos = slice_y
for(i in seq_len(nr_slice)) {
slice_leaf_pos[i] = slice_leaf_pos[i] - slice_height[i]*p[i]
}
row_dend_slice = merge_dendrogram(row_dend_slice, object@row_dend_list, only_parent = TRUE)
row_dend_slice = adjust_dend_by_x(row_dend_slice, slice_leaf_pos)
grid.dendrogram(row_dend_slice, facing = ifelse(row_dend_side == "left", "right", "left"))
popViewport()
}
upViewport()
})
}
##########################################
## dend on top or bottom
show_column_dend = object@column_dend_param$show
column_dend_side = object@column_dend_param$side
column_dend_height = object@column_dend_param$height
column_dend_slice = object@column_dend_slice
if(show_column_dend) {
if(column_dend_side == "top") {
object@layout$layout_size$column_dend_top_height = column_dend_height
object@layout$layout_index = rbind(object@layout$layout_index, column_dend_top = heatmap_layout_index("column_dend_top"))
} else {
object@layout$layout_size$column_dend_bottom_height = column_dend_height
object@layout$layout_index = rbind(object@layout$layout_index, column_dend_bottom = heatmap_layout_index("column_dend_bottom"))
}
column_dend_max_height = dend_heights(column_dend_slice) + max(dend_heights(object@column_dend_list))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
if(column_dend_side == "top") {
pushViewport(viewport(y = ht_opt$DENDROGRAM_PADDING, height = unit(1, "npc") - ht_opt$DENDROGRAM_PADDING, just = "bottom"))
} else {
pushViewport(viewport(y = unit(0, "npc"), height = unit(1, "npc") - ht_opt$DENDROGRAM_PADDING, just = "bottom"))
}
for(i in seq_len(nc_slice)) {
draw_dend(object, k = i, which = "column", x = slice_x[i], width = slice_width[i], just = "left",
max_height = column_dend_max_height)
}
if(nc_slice > 1) {
if(column_dend_side == "top") {
pushViewport(viewport(yscale = c(0, column_dend_max_height)))
} else {
pushViewport(viewport(yscale = c(0, column_dend_max_height)))
}
p = sapply(object@column_dend_list, function(x) {
attr(x, "x")/nobs(x)
})
nb = sapply(object@column_dend_list, nobs)
slice_leaf_pos = slice_x
for(i in seq_len(nc_slice)) {
slice_leaf_pos[i] = slice_leaf_pos[i] + slice_width[i]*p[i]
}
column_dend_slice = merge_dendrogram(column_dend_slice, object@column_dend_list, only_parent = TRUE)
column_dend_slice = adjust_dend_by_x(column_dend_slice, slice_leaf_pos)
grid.dendrogram(column_dend_slice, facing = ifelse(column_dend_side == "top", "bottom", "top"))
popViewport()
}
upViewport()
})
}
#######################################
## row_names on left or right
row_names_side = object@row_names_param$side
show_row_names = object@row_names_param$show
row_names_anno = object@row_names_param$anno
if(show_row_names) {
row_names_width = row_names_anno@width + ht_opt$DIMNAME_PADDING*2
row_names_width = min(row_names_width, object@row_names_param$max_width)
if(row_names_side == "left") {
object@layout$layout_size$row_names_left_width = row_names_width
object@layout$layout_index = rbind(object@layout$layout_index, row_names_left = heatmap_layout_index("row_names_left"))
} else {
object@layout$layout_size$row_names_right_width = row_names_width
object@layout$layout_index = rbind(object@layout$layout_index, row_names_right = heatmap_layout_index("row_names_right"))
}
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nr_slice)) {
draw_dimnames(object, k = i, which = "row", y = slice_y[i],
height = slice_height[i], width = unit(1, "npc") - ht_opt$DIMNAME_PADDING*2, just = "top")
}
})
}
#########################################
## column_names on top or bottom
column_names_side = object@column_names_param$side
show_column_names = object@column_names_param$show
column_names_anno = object@column_names_param$anno
if(show_column_names) {
column_names_height = column_names_anno@height + ht_opt$DIMNAME_PADDING*2
column_names_height = min(column_names_height, object@column_names_param$max_height)
if(column_names_side == "top") {
object@layout$layout_size$column_names_top_height = column_names_height
object@layout$layout_index = rbind(object@layout$layout_index, column_names_top = heatmap_layout_index("column_names_top"))
} else {
object@layout$layout_size$column_names_bottom_height = column_names_height
object@layout$layout_index = rbind(object@layout$layout_index, column_names_bottom = heatmap_layout_index("column_names_bottom"))
}
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nc_slice)) {
draw_dimnames(object, k = i, which = "column", x = slice_x[i],
width = slice_width[i], height = unit(1, "npc") - ht_opt$DIMNAME_PADDING*2, just = "left")
}
})
}
##########################################
## annotation on top
annotation = object@top_annotation
annotation_height = object@top_annotation_param$height
if(!is.null(annotation)) {
if(length(annotation@anno_list) > 0) {
object@layout$layout_size$column_anno_top_height = annotation_height
object@layout$layout_index = rbind(object@layout$layout_index, column_anno_top = heatmap_layout_index("column_anno_top"))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nc_slice)) {
draw_annotation(object, k = i, which = "top", x = slice_x[i], width = slice_width[i],
y = ht_opt$COLUMN_ANNO_PADDING, height = unit(1, "npc") - ht_opt$COLUMN_ANNO_PADDING,
just = c("left", "bottom"))
}
})
}
}
##########################################
## annotation on bottom
annotation = object@bottom_annotation
annotation_height = object@bottom_annotation_param$height
if(!is.null(annotation)) {
if(length(annotation@anno_list) > 0) {
object@layout$layout_size$column_anno_bottom_height = annotation_height
object@layout$layout_index = rbind(object@layout$layout_index, column_anno_bottom = heatmap_layout_index("column_anno_bottom"))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nc_slice)) {
draw_annotation(object, k = i, which = "bottom", x = slice_x[i], width = slice_width[i],
y = unit(0, "npc"), height = unit(1, "npc") - ht_opt$COLUMN_ANNO_PADDING,
just = c("left", "bottom"))
}
})
}
}
##########################################
## annotation on left
annotation = object@left_annotation
annotation_width = object@left_annotation_param$width
if(!is.null(annotation)) {
if(length(annotation@anno_list) > 0) {
object@layout$layout_size$row_anno_left_width = annotation_width
object@layout$layout_index = rbind(object@layout$layout_index, row_anno_left = heatmap_layout_index("row_anno_left"))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nr_slice)) {
draw_annotation(object, k = i, which = "left", y = slice_y[i], height = slice_height[i],
x = unit(0, "npc"), width = unit(1, "npc") - ht_opt$ROW_ANNO_PADDING,
just = c("left", "top"))
}
}
)
}
}
##########################################
## annotation on right
annotation = object@right_annotation
annotation_width = object@right_annotation_param$width
if(!is.null(annotation)) {
if(length(annotation@anno_list) > 0) {
object@layout$layout_size$row_anno_right_width = annotation_width
object@layout$layout_index = rbind(object@layout$layout_index, row_anno_right = heatmap_layout_index("row_anno_right"))
object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {
for(i in seq_len(nr_slice)) {
draw_annotation(object, k = i, which = "right", y = slice_y[i], height = slice_height[i],
x = ht_opt$ROW_ANNO_PADDING, width = unit(1, "npc") - ht_opt$ROW_ANNO_PADDING,
just = c("left", "top"))
}
})
}
}
layout_size = object@layout$layout_size
if(is_abs_unit(object@heatmap_param$width)) {
# recalcualte the width of heatmap body
object@matrix_param$width = object@heatmap_param$width -
sum(layout_size$row_title_left_width,
layout_size$row_dend_left_width,
layout_size$row_anno_left_width,
layout_size$row_names_left_width,
layout_size$row_dend_right_width,
layout_size$row_anno_right_width,
layout_size$row_names_right_width,
layout_size$row_title_right_width)
} else if(is_abs_unit(object@matrix_param$width)) { # e.g. unit(1, "npc")
object@heatmap_param$width = sum(
layout_size$row_title_left_width,
layout_size$row_dend_left_width,
layout_size$row_names_left_width,
layout_size$row_dend_right_width,
layout_size$row_names_right_width,
layout_size$row_title_right_width,
layout_size$row_anno_left_width,
layout_size$row_anno_right_width
) + object@matrix_param$width
if(nr_slice > 1) {
object@heatmap_param$width = object@heatmap_param$width + sum(row_gap[seq_len(nr_slice-1)])
}
} else {
object@heatmap_param$width = unit(1, "npc")
}
if(is_abs_unit(object@heatmap_param$height)) {
object@matrix_param$height = object@heatmap_param$height -
sum(layout_size$column_title_top_height,
layout_size$column_dend_top_height,
layout_size$column_anno_top_height,
layout_size$column_names_top_height,
layout_size$column_title_bottom_height,
layout_size$column_dend_bottom_height,
layout_size$column_anno_bottom_height,
layout_size$column_names_bottom_height)
} else if(is_abs_unit(object@matrix_param$height)) {
object@heatmap_param$height = sum(
layout_size$column_title_top_height,
layout_size$column_dend_top_height,
layout_size$column_anno_top_height,
layout_size$column_names_top_height,
layout_size$column_title_bottom_height,
layout_size$column_dend_bottom_height,
layout_size$column_anno_bottom_height,
layout_size$column_names_bottom_height
) + object@matrix_param$height
if(nc_slice > 1) {
object@heatmap_param$height = object@heatmap_param$height + sum(column_gap[seq_len(nc_slice-1)])
}
} else {
object@heatmap_param$height = unit(1, "npc")
}
object@heatmap_param$width_is_absolute_unit = is_abs_unit(object@heatmap_param$width)
object@heatmap_param$height_is_absolute_unit = is_abs_unit(object@heatmap_param$height)
object@layout$initialized = TRUE
return(object)
})
# == title
# Draw the Single Heatmap with Defaults
#
# == param
# -object A `Heatmap-class` object.
#
# == details
# It actually calls `draw,Heatmap-method`, but only with default parameters. If users want to customize the heatmap,
# they can pass parameters directly to `draw,Heatmap-method`.
#
# == value
# The `HeatmapList-class` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "show",
signature = "Heatmap",
definition = function(object) {
draw(object)
})
# == title
# Add Heatmap to the Heatmap List
#
# == param
# -object A `Heatmap-class` object.
# -x a `Heatmap-class` object, a `HeatmapAnnotation-class` object or a `HeatmapList-class` object.
# -direction Whether the heatmap is added horizontal or vertically?
#
# == details
# There is a shortcut function ``+.AdditiveUnit``.
#
# == value
# A `HeatmapList-class` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "add_heatmap",
signature = "Heatmap",
definition = function(object, x, direction = c("horizontal", "vertical")) {
direction = match.arg(direction)[1]
ht_list = new("HeatmapList")
ht_list@direction = direction
ht_list = add_heatmap(ht_list, object, direction = direction)
ht_list = add_heatmap(ht_list, x, direction = direction)
return(ht_list)
})
# == title
# Widths of Heatmap Components
#
# == param
# -object A `Heatmap-class` object.
# -k Which components in the heatmap. The value should numeric indices or the names
# of the corresponding row component. See **Detials**.
#
# == details
# All row components are: ``row_title_left``, ``row_dend_left``, ``row_names_left``, ``row_anno_left``,
# ``heatmap_body``, ``row_anno_right``, ``row_names_right``, ``row_dend_right``, ``row_title_right``.
#
# This function is only for internal use.
#
# == value
# A `grid::unit` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "component_width",
signature = "Heatmap",
definition = function(object, k = HEATMAP_LAYOUT_ROW_COMPONENT) {
if(is.numeric(k)) {
component_name = names(HEATMAP_LAYOUT_ROW_COMPONENT)[k]
} else {
component_name = k
}
# this function is used for grid.layout, so null unit is allowed
.single_unit = function(nm) {
if(nm == "heatmap_body") {
object@matrix_param$width
} else {
object@layout$layout_size[[paste0(nm, "_width")]]
}
}
do.call("unit.c", lapply(component_name, .single_unit))
})
# == title
# Heights of Heatmap Components
#
# == param
# -object A `Heatmap-class` object.
# -k Which components in the heatmap. The value should numeric indices or the names
# of the corresponding column component. See **Detials**.
#
# == detail
# All column components are: ``column_title_top``, ``column_dend_top``, ``column_names_top``,
# ``column_anno_top``, ``heatmap_body``, ``column_anno_bottom``, ``column_names_bottom``,
# ``column_dend_bottom``, ``column_title_bottom``.
#
# This function is only for internal use.
#
# == value
# A `grid::unit` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "component_height",
signature = "Heatmap",
definition = function(object, k = HEATMAP_LAYOUT_COLUMN_COMPONENT) {
if(is.numeric(k)) {
component_name = names(HEATMAP_LAYOUT_COLUMN_COMPONENT)[k]
} else {
component_name = k
}
# this function is used for grid.layout, so null unit is allowed
.single_unit = function(nm) {
if(nm == "heatmap_body") {
object@matrix_param$height
} else {
object@layout$layout_size[[paste0(nm, "_height")]]
}
}
do.call("unit.c", lapply(component_name, .single_unit))
})
has_component = function(object, component) {
m = object@layout$layout_index
ind = heatmap_layout_index(component)
any(m[, 1] == ind[1] & m[, 2] == ind[2])
}
HEATMAP_LAYOUT_COLUMN_COMPONENT = 1:9
names(HEATMAP_LAYOUT_COLUMN_COMPONENT) = c("column_title_top", "column_dend_top", "column_names_top", "column_anno_top",
"heatmap_body", "column_anno_bottom", "column_names_bottom", "column_dend_bottom", "column_title_bottom")
HEATMAP_LAYOUT_ROW_COMPONENT = 1:9
names(HEATMAP_LAYOUT_ROW_COMPONENT) = c("row_title_left", "row_dend_left", "row_names_left", "row_anno_left",
"heatmap_body", "row_anno_right", "row_names_right", "row_dend_right", "row_title_right")
heatmap_layout_index = function(nm) {
if(grepl("column", nm)) {
ind = c(HEATMAP_LAYOUT_COLUMN_COMPONENT[nm], HEATMAP_LAYOUT_ROW_COMPONENT["heatmap_body"])
} else if(grepl("row", nm)) {
ind = c(HEATMAP_LAYOUT_COLUMN_COMPONENT["heatmap_body"], HEATMAP_LAYOUT_ROW_COMPONENT[nm])
} else if(nm == "heatmap_body") { # heatmap_body
ind = c(HEATMAP_LAYOUT_COLUMN_COMPONENT["heatmap_body"], HEATMAP_LAYOUT_ROW_COMPONENT["heatmap_body"])
}
names(ind) = c("layout.pos.row", "layout.pos.col")
return(ind)
}
# == title
# Set Width of Heatmap Component
#
# == param
# -object A `Heatmap-class` object.
# -k Which row component? The value should a numeric index or the name
# of the corresponding row component. See **Detials**.
# -v width of the component, a `grid::unit` object.
#
# == detail
# All row components are: ``row_title_left``, ``row_dend_left``, ``row_names_left``, ``row_anno_left``,
# ``heatmap_body``, ``row_anno_right``, ``row_names_right``, ``row_dend_right``, ``row_title_right``.
#
# This function is only for internal use.
#
# == value
# The `Heatmap-class` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "set_component_width",
signature = "Heatmap",
definition = function(object, k, v) {
if(is.numeric(k)) {
nm = names(HEATMAP_LAYOUT_ROW_COMPONENT)[k]
} else {
nm = k
}
object@layout$layout_size[[ paste0(nm, "_width") ]] = v
if(is_abs_unit(object@matrix_param$width)) {
object@heatmap_param$width = sum(component_width(object))
}
return(object)
})
# == title
# Set Height of Heatmap Component
#
# == param
# -object A `Heatmap-class` object.
# -k Which column component? The value should a numeric index or the name
# of the corresponding column component. See **Detials**.
# -v Height of the component, a `grid::unit` object.
#
# == detail
# All column components are: ``column_title_top``, ``column_dend_top``, ``column_names_top``,
# ``column_anno_top``, ``heatmap_body``, ``column_anno_bottom``, ``column_names_bottom``,
# ``column_dend_bottom``, ``column_title_bottom``.
#
# This function is only for internal use.
#
# == value
# The `Heatmap-class` object.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "set_component_height",
signature = "Heatmap",
definition = function(object, k, v) {
if(is.numeric(k)) {
nm = names(HEATMAP_LAYOUT_COLUMN_COMPONENT)[k]
} else {
nm = k
}
object@layout$layout_size[[ paste0(nm, "_height") ]] = v
if(is_abs_unit(object@matrix_param$height)) {
object@heatmap_param$height = sum(component_height(object))
}
return(object)
})
