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# == title
# Draw Heatmap Body
#
# == param
# -object A `Heatmap-class` object.
# -kr Row slice index.
# -kc Column slice index.
# -... Pass to `grid::viewport` which includes the slice of heatmap body.
#
# == details
# A viewport is created which contains subset rows and columns of the heatmap.
#
# This function is only for internal use.
#
# == value
# This function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "draw_heatmap_body",
signature = "Heatmap",
definition = function(object, kr = 1, kc = 1, ...) {
if(ncol(object@matrix) == 0 || nrow(object@matrix) == 0) {
return(invisible(NULL))
}
row_order = object@row_order_list[[kr]]
column_order = object@column_order_list[[kc]]
gp = object@matrix_param$gp
border = object@matrix_param$border
use_raster = object@heatmap_param$use_raster
raster_device = object@heatmap_param$raster_device
raster_quality = object@heatmap_param$raster_quality
raster_device_param = object@heatmap_param$raster_device_param
raster_by_magick = object@heatmap_param$raster_by_magick
raster_magick_filter = object@heatmap_param$raster_magick_filter
if(length(raster_device_param) == 0) raster_device_param = list()
pushViewport(viewport(name = paste(object@name, "heatmap_body", kr, kc, sep = "_"), ...))
mat = object@matrix[row_order, column_order, drop = FALSE]
oe = try(col_matrix <- map_to_colors(object@matrix_color_mapping, mat), silent = TRUE)
if(inherits(oe, "try-error")) {
col_matrix = matrix(NA, nrow = nrow(mat), ncol = ncol(mat))
}
nc = ncol(mat)
nr = nrow(mat)
x = (seq_len(nc) - 0.5) / nc
y = (rev(seq_len(nr)) - 0.5) / nr
expand_index = expand.grid(seq_len(nr), seq_len(nc))
cell_fun = object@matrix_param$cell_fun
layer_fun = object@matrix_param$layer_fun
if(!is.null(cell_fun)) {
use_raster = FALSE
}
if(identical(object@matrix_param$gp$type, "none")) {
use_raster = FALSE
}
if(use_raster) {
# write the image into a temporary file and read it back
device_info = switch(raster_device,
png = c("grDevices", "png", "readPNG"),
jpeg = c("grDevices", "jpeg", "readJPEG"),
tiff = c("grDevices", "tiff", "readTIFF"),
CairoPNG = c("Cairo", "png", "readPNG"),
CairoJPEG = c("Cairo", "jpeg", "readJPEG"),
CairoTIFF = c("Cairo", "tiff", "readTIFF"),
agg_png = c("ragg", "png", "readPNG")
)
if(!requireNamespace(device_info[1])) {
stop_wrap(paste0("Need ", device_info[1], " package to write image."))
}
if(!requireNamespace(device_info[2])) {
stop_wrap(paste0("Need ", device_info[2], " package to read image."))
}
if(raster_device %in% c("png", "jpeg", "tiff")) {
if(! "type" %in% names(raster_device_param)) {
if(capabilities("cairo")) {
raster_device_param$type = "cairo"
}
}
}
# can we get the size of the heatmap body?
heatmap_width_pt = max(1, ceiling(convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)))
heatmap_height_pt = max(1, ceiling(convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)))
if(raster_quality < 1) raster_quality = 1
heatmap_width_pt = ceiling(heatmap_width_pt * raster_quality)
heatmap_height_pt = ceiling(heatmap_height_pt * raster_quality)
matrix_is_resized = FALSE
# resize on the matrix
raster_resize_mat = object@heatmap_param$raster_resize_mat
if(!identical(raster_resize_mat, FALSE)) {
if(is.logical(raster_resize_mat)) {
raster_resize_mat_fun = function(x) mean(x, na.rm = TRUE)
} else {
if(!inherits(raster_resize_mat, "function")) {
stop_wrap("`raster_resize_mat` should be set as logical scalar or a function.")
}
raster_resize_mat_fun = raster_resize_mat
}
if(heatmap_width_pt < nc && heatmap_height_pt < nr) {
mat2 = resize_matrix(mat, nr = heatmap_height_pt, nc = heatmap_width_pt, fun = raster_resize_mat_fun)
matrix_is_resized = TRUE
} else if(heatmap_width_pt < nc) {
mat2 = resize_matrix(mat, nr = nr, nc = heatmap_width_pt, fun = raster_resize_mat_fun)
matrix_is_resized = TRUE
} else if(heatmap_height_pt < nr) {
mat2 = resize_matrix(mat, nr = heatmap_height_pt, nc = nc, fun = raster_resize_mat_fun)
matrix_is_resized = TRUE
}
}
if(matrix_is_resized) {
raster_by_magick = FALSE
}
temp_dir = tempdir()
temp_image = tempfile(pattern = paste0(".heatmap_body_", digest::digest(object@name), "_", kr, "_", kc), tmpdir = temp_dir, fileext = paste0(".", device_info[2]))
device_fun = getFromNamespace(raster_device, ns = device_info[1])
if(raster_by_magick) {
temp_image_width = ceiling(max(heatmap_width_pt, nc, 1))
temp_image_height = ceiling(max(heatmap_height_pt, nr, 1))
} else if(matrix_is_resized) {
temp_image_width = ceiling(max(heatmap_width_pt, 1))
temp_image_height = ceiling(max(heatmap_height_pt, 1))
} else {
temp_image_width = ceiling(max(heatmap_width_pt, 1))
temp_image_height = ceiling(max(heatmap_height_pt, 1))
}
temp_image_width = as.integer(temp_image_width)
temp_image_height = as.integer(temp_image_height)
if(!is.na(ht_opt$raster_temp_image_max_width)) {
temp_image_width = min(temp_image_width, ht_opt$raster_temp_image_max_width)
}
if(!is.na(ht_opt$raster_temp_image_max_height)) {
temp_image_height = min(temp_image_height, ht_opt$raster_temp_image_max_height)
}
oe = try(do.call(device_fun, c(list(filename = temp_image,
width = temp_image_width, height = temp_image_height), raster_device_param)))
if(inherits(oe, "try-error")) {
stop_wrap(qq("The size of the temporary image for rasterization is too huge (@{temp_image_width} x @{temp_image_height} px) that it is cannot be handled by the device function `@{device_info[1]}:@{raster_device}()`. Please reduce the maximal size of temporary image by setting proper values for `ht_opt$raster_temp_image_max_width` and `ht_opt$raster_temp_image_max_height`."))
}
if(object@heatmap_param$verbose) {
qqcat("saving into a temp image (.@{device_info[2]}) with size @{temp_image_width}x@{temp_image_height}px.\n")
}
if(matrix_is_resized) {
if(object@heatmap_param$verbose) {
qqcat("resize the matrix from (@{nrow(mat)}x@{ncol(mat)}) to (@{nrow(mat2)}x@{ncol(mat2)}).\n")
}
col_matrix2 = map_to_colors(object@matrix_color_mapping, mat2)
nc2 = ncol(mat2)
nr2 = nrow(mat2)
x2 = (seq_len(nc2) - 0.5) / nc2
y2 = (rev(seq_len(nr2)) - 0.5) / nr2
expand_index2 = expand.grid(seq_len(nr2), seq_len(nc2))
grid.rect(x2[expand_index2[[2]]], y2[expand_index2[[1]]], width = unit(1/nc2, 'npc'), height = unit(1/nr2, 'npc'), gp = do.call('gpar', c(list(fill = col_matrix2), gp)))
} else {
grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, 'npc'), height = unit(1/nr, 'npc'), gp = do.call('gpar', c(list(fill = col_matrix), gp)))
}
if(is.function(layer_fun)) {
if(length(as.list(formals(layer_fun))) == 7) {
layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ],
unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),
unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),
as.vector(col_matrix))
} else {
layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ],
unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),
unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),
as.vector(col_matrix), kr, kc)
}
}
dev.off2()
if(object@heatmap_param$verbose) {
qqcat("resize the temp image to a size @{heatmap_width_pt}x@{heatmap_height_pt}px.\n")
}
if(raster_by_magick) {
if(object@heatmap_param$verbose) {
qqcat("image is read by magick.\n")
}
if(!requireNamespace("magick")) {
stop_wrap("'magick' package should be installed.")
}
image = magick::image_read(temp_image)
image = magick::image_resize(image, paste0(heatmap_width_pt, "x", heatmap_height_pt, "!"), filter = raster_magick_filter)
image = as.raster(image)
} else {
if(object@heatmap_param$verbose) {
qqcat("image is read by @{device_info[2]}::@{device_info[3]}\n")
}
image = getFromNamespace(device_info[3], ns = device_info[2])(temp_image)
}
# validate image, there might be white horizontal lines and vertical lines
# image = validate_raster_matrix(image, mat, object@matrix_color_mapping)
grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"), interpolate = FALSE)
### only for testing the temp image size ###
if(ht_opt("__export_image_size__")) {
if(inherits(image, "magick-image")) {
image = as.raster(image)
} else {
tf = tempfile()
png(tf, width = heatmap_width_pt, height = heatmap_height_pt)
grid.raster(image, width = unit(1, "npc"), height = unit(1, "npc"))
dev.off()
image = as.raster(png::readPNG(tf))
file.remove(tf)
}
attr(image, "width") = heatmap_width_pt
attr(image, "height") = heatmap_height_pt
# assign(".image", image, envir = .GlobalEnv)
}
########################
file.remove(temp_image)
} else {
if(any(names(gp) %in% c("type"))) {
if(gp$type == "none") {
} else {
grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))
}
} else {
grid.rect(x[expand_index[[2]]], y[expand_index[[1]]], width = unit(1/nc, "npc"), height = unit(1/nr, "npc"), gp = do.call("gpar", c(list(fill = col_matrix), gp)))
}
if(is.function(cell_fun)) {
for(i in seq_len(nr)) {
for(j in seq_len(nc)) {
cell_fun(column_order[j], row_order[i], unit(x[j], "npc"), unit(y[i], "npc"),
unit(1/nc, "npc"), unit(1/nr, "npc"),
col_matrix[i, j])
}
}
}
if(is.function(layer_fun)) {
if(length(as.list(formals(layer_fun))) == 7) {
layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ],
unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),
unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),
as.vector(col_matrix))
} else {
layer_fun(column_order[ expand_index[[2]] ], row_order[ expand_index[[1]] ],
unit(x[expand_index[[2]]], "npc"), unit(y[expand_index[[1]]], "npc"),
unit(rep(1/nc, nrow(expand_index)), "npc"), unit(rep(1/nr, nrow(expand_index)), "npc"),
as.vector(col_matrix), kr, kc)
}
}
}
if(!(identical(border, FALSE) || identical(border, NA))) {
border_gp = object@matrix_param$border_gp
if(!identical(border, TRUE)) {
border_gp$col = border
}
if("fill" %in% names(border_gp)) {
message_wrap("`fill` is ignored in `border_gp`. The value for `fill` is always 'transparent'.")
}
border_gp$fill = "transparent"
grid.rect(gp = border_gp)
}
upViewport()
})
# check white lines in the RGB matrix, and re-fill the color from mat with color_mapping
# careful: row orders of rgb and mat are reversed
# rgb: values change from 0 to 1
validate_raster_matrix = function(rgb, mat, col_mapping) {
if(is.character(rgb)) {
dim = dim(rgb)
x = col2rgb(rgb)/255
rgb = array(dim = c(dim, 3))
rgb[, , 1] = matrix(x[1, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)
rgb[, , 2] = matrix(x[2, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)
rgb[, , 3] = matrix(x[3, ], nrow = dim[1], ncol = dim[2], byrow = TRUE)
}
# check rows
white_row = NULL
white_column = NULL
if(any( abs(rgb[, 1, 1] - 1) < 1e-10 & abs(rgb[, 1, 2] - 1) < 1e-10 & abs(rgb[, 1, 3] - 1)< 1e-10 )) {
white_row = which( abs(rowMeans(rgb[, , 1]) - 1) < 1e-10 &
abs(rowMeans(rgb[, , 2]) - 1) < 1e-10 &
abs(rowMeans(rgb[, , 3]) - 1) < 1e-10 )
}
if(any( abs(rgb[1, , 1] - 1) < 1e-10 & abs(rgb[1, , 2] - 1) < 1e-10 & abs(rgb[1, , 3] - 1)< 1e-10 )) {
white_column = which( abs(colMeans(rgb[, , 1]) - 1) < 0.1 &
abs(colMeans(rgb[, , 2]) - 1) < 0.1 &
abs(colMeans(rgb[, , 3]) - 1) < 0.1 )
}
# estimate while rows and columns
rgb
}
is_windows = function() {
tolower(.Platform$OS.type) == "windows"
}
R_binary = function() {
R_exe = ifelse(is_windows(), "R.exe", "R")
return(file.path(R.home("bin"), R_exe))
}
# == title
# Draw Heatmap Dendrograms
#
# == param
# -object A `Heatmap-class` object.
# -which Are the dendrograms put on the row or on the column of the heatmap?
# -k Slice index.
# -max_height maximal height of dendrogram.
# -... Pass to `grid::viewport` which includes the complete heatmap dendrograms.
#
# == details
# A viewport is created which contains dendrograms.
#
# This function is only for internal use.
#
# == value
# This function returns no value.
#
# == seealso
# `grid.dendrogram`
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "draw_dend",
signature = "Heatmap",
definition = function(object,
which = c("row", "column"), k = 1, max_height = NULL, ...) {
which = match.arg(which)[1]
side = switch(which,
"row" = object@row_dend_param$side,
"column" = object@column_dend_param$side)
dend = switch(which,
"row" = object@row_dend_list[[k]],
"column" = object@column_dend_list[[k]])
gp = switch(which,
"row" = object@row_dend_param$gp,
"column" = object@column_dend_param$gp)
if(length(dend) == 0) {
return(invisible(NULL))
}
if(is.null(dend)) return(invisible(NULL))
if(nobs(dend) <= 1) {
return(invisible(NULL))
}
if(is.null(max_height)) {
max_height = dend_heights(dend)
}
if(max_height == 0) max_height = 1
if(side %in% c("left", "right")) {
xscale = c(0, max_height)
yscale = c(0, nobs(dend))
width = unit(1, "npc")
height = unit(1, "npc")
name = paste(object@name, "dend_row", k, sep = "_")
} else {
xscale = c(0, nobs(dend))
yscale = c(0, max_height)
height = unit(1, "npc")
width = unit(1, "npc")
name = paste(object@name, "dend_column", k, sep = "_")
}
pushViewport(viewport(...))
pushViewport(viewport(name = name, xscale = xscale, yscale = yscale, width = width, height = height))
if(side == "left") {
grid.dendrogram(dend, gp = gp, facing = "right", order = "reverse")
} else if(side == "right") {
grid.dendrogram(dend, gp = gp, facing = "left", order = "reverse")
} else if(side == "top") {
grid.dendrogram(dend, gp = gp, facing = "bottom")
} else if(side == "bottom") {
grid.dendrogram(dend, gp = gp, facing = "top")
}
upViewport()
upViewport()
})
# == title
# Draw row names or column names
#
# == param
# -object A `Heatmap-class` object.
# -which Are the names put on the row or on the column of the heatmap?
# -k Slice index.
# -... Pass to `grid::viewport` which includes the complete heatmap row/column names.
#
# == details
# A viewport is created which contains row names or column names.
#
# This function is only for internal use.
#
# == value
# This function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "draw_dimnames",
signature = "Heatmap",
definition = function(object,
which = c("row", "column"), k = 1, ...) {
which = match.arg(which)[1]
anno = switch(which,
"row" = object@row_names_param$anno,
"column" = object@column_names_param$anno)
ind = switch(which,
"row" = object@row_order_list[[k]],
"column" = object@column_order_list[[k]])
pushViewport(viewport(name = paste(object@name, which, "names", k, sep = "_"), ...))
if(which == "row") {
if(object@row_names_param$side == "right" ) {
x = unit(0, "npc")
y = unit(0.5, "npc")
just = "left"
} else {
x = unit(1, "npc")
y = unit(0.5, "npc")
just = "right"
}
} else {
if(object@column_names_param$side == "top") {
x = unit(0.5, "npc")
y = unit(0, "npc")
just = "bottom"
} else {
x = unit(0.5, "npc")
y = unit(1, "npc")
just = "top"
}
}
draw(anno, index = ind, x = x, y = y, just = just)
upViewport()
})
# == title
# Draw Heatmap Title
#
# == param
# -object A `Heatmap-class` object.
# -which Is title put on the row or on the column of the heatmap?
# -k Slice index.
# -... Pass to `grid::viewport` which includes the complete heatmap title.
#
# == details
# A viewport is created which contains heatmap title.
#
# This function is only for internal use.
#
# == value
# This function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "draw_title",
signature = "Heatmap",
definition = function(object,
which = c("row", "column"), k = 1, ...) {
which = match.arg(which)[1]
side = switch(which,
"row" = object@row_title_param$side,
"column" = object@column_title_param$side)
gp = switch(which,
"row" = object@row_title_param$gp,
"column" = object@column_title_param$gp)
gp = subset_gp(gp, k)
title = switch(which,
"row" = object@row_title[k],
"column" = object@column_title[k])
rot = switch(which,
"row" = object@row_title_param$rot,
"column" = object@column_title_param$rot)
just = switch(which,
"row" = object@row_title_param$just,
"column" = object@column_title_param$just)
if(!is.null(ht_opt$TITLE_PADDING)) {
title_padding = ht_opt$TITLE_PADDING
} else {
title_padding = unit(c(0, 0), "points")
title_padding[1] = title_padding[1] + unit(5.5, "points") +
convertHeight(grobDescent(textGrob(label = "jA", gp = gp)), "inches")
}
if(which == "row") {
pushViewport(viewport(name = paste(object@name, "row_title", k, sep = "_"), clip = FALSE, ...))
gp2 = gp
if("border" %in% names(gp2)) gp2$col = gp2$border
if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)
if(side == "left") {
grid.text(title, x = unit(1, "npc") - title_padding[1], rot = rot, just = just, gp = gp)
} else {
grid.text(title, x = title_padding[1], rot = rot, just = just, gp = gp)
}
upViewport()
} else {
pushViewport(viewport(name = paste(object@name, "column_title", k, sep = "_"), clip = FALSE, ...))
gp2 = gp
if("border" %in% names(gp2)) gp2$col = gp2$border
if(any(c("border", "fill") %in% names(gp2))) grid.rect(gp = gp2)
if(side == "top") {
grid.text(title, y = title_padding[1], rot = rot, just = just, gp = gp)
} else {
grid.text(title, y = unit(1, "npc") - title_padding[1], rot = rot, just = just, gp = gp)
}
upViewport()
}
})
# == title
# Draw Heatmap Annotations on the Heatmap
#
# == param
# -object A `Heatmap-class` object.
# -which The position of the heamtap annotation.
# -k Slice index.
# -... Pass to `grid::viewport` which includes the complete heatmap annotation.
#
# == details
# A viewport is created which contains column/top annotations.
#
# The function calls `draw,HeatmapAnnotation-method` to draw the annotations.
#
# This function is only for internal use.
#
# == value
# This function returns no value.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
setMethod(f = "draw_annotation",
signature = "Heatmap",
definition = function(object, which = c("top", "bottom", "left", "right"), k = 1, ...) {
which = match.arg(which)[1]
annotation = switch(which,
top = object@top_annotation,
bottom = object@bottom_annotation,
left = object@left_annotation,
right = object@right_annotation)
# if there is no annotation, draw nothing
if(is.null(annotation)) {
return(invisible(NULL))
}
if(which %in% c("top", "bottom")) {
index = object@column_order_list[[k]]
n = length(object@column_order_list)
} else {
index = object@row_order_list[[k]]
n = length(object@row_order_list)
}
## deal with the special anno_mark
anno_mark_param = list()
if(which %in% c("left", "right")) {
slice_y = object@layout$slice$y
n_slice = length(slice_y)
slice_height = object@layout$slice$height
if(n_slice > 1) {
all_anno_type = anno_type(annotation)
if(any(c("anno_zoom", "anno_mark") %in% all_anno_type)) {
## only make the anno_mark annotation
ro_lt = object@row_order_list
# calcualte the position of each row with taking "gaps" into account
.scale = c(0, 1)
.pos = NULL
for(i in seq_along(ro_lt)) {
# assume slices are align to top `slice_just` contains "top"
.pos1 = slice_y[i] - (seq_along(ro_lt[[i]]) - 0.5)/length(ro_lt[[i]]) * slice_height[i]
.pos1 = convertY(.pos1, "native", valueOnly = TRUE)
.pos = c(.pos, .pos1)
}
anno_mark_param$.scale = .scale
anno_mark_param$.pos = .pos
anno_mark_param$index = unlist(ro_lt)
if(abs(par("din")[2] - grDevices::dev.size("in")[2]) < 1e-6) {
anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")
} else {
anno_mark_param$vp_height = convertHeight(unit(1, "npc"), "cm")*(par("din")[2]/grDevices::dev.size("in")[2])*0.9742
}
anno_mark_param$vp_width = unit(1, "npc")
anno_mark_param$vp_just = "top"
anno_mark_param$vp_x = unit(0.5, "npc")
anno_mark_param$vp_y = unit(1, "npc")
}
}
} else {
slice_x = object@layout$slice$x
n_slice = length(slice_x)
slice_width = object@layout$slice$width
if(n_slice > 1) {
all_anno_type = anno_type(annotation)
if(any(c("anno_zoom", "anno_mark") %in% all_anno_type)) {
## only make the anno_mark annotation
co_lt = object@column_order_list
.scale = c(0, 1)
.pos = NULL
for(i in seq_along(co_lt)) {
.pos1 = slice_x[i] + (seq_along(co_lt[[i]]) - 0.5)/length(co_lt[[i]]) * slice_width[i]
.pos1 = convertX(.pos1, "native", valueOnly = TRUE)
.pos = c(.pos, .pos1)
}
anno_mark_param$.scale = .scale
anno_mark_param$.pos = .pos
anno_mark_param$index = unlist(co_lt)
anno_mark_param$vp_height = unit(1, "npc")
if(abs(par("din")[1] - grDevices::dev.size("in")[1]) < 1e-6) {
anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")
} else {
anno_mark_param$vp_width = convertWidth(unit(1, "npc"), "cm")*(par("din")[1]/grDevices::dev.size("in")[1])*0.945
}
anno_mark_param$vp_just = "left"
anno_mark_param$vp_x = unit(0, "npc")
anno_mark_param$vp_y = unit(0.5, "npc")
}
}
}
pushViewport(viewport(...))
draw(annotation, index = index, k = k, n = n, anno_mark_param = anno_mark_param)
upViewport()
})
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