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# == title
# Draw 3D bars
#
# == param
# -x x coordinate of the center point in the bottom face.
# -y y coordinate of the center point in the bottom face.
# -w Width of the botton face.
# -h Height of the botton face.
# -l Length of the bars (in the z-direction).
# -theta The angle for the projection.
# -default.units Units.
# -fill Filled colors for the bars.
# -col Border colors.
#
# == example
# grid.newpage()
# bar3D(c(0.3, 0.7), 0.5, 0.2, 0.2, 0.2, fill = 2:3)
#
bar3D = function(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black") {
if(!is.unit(x)) x = unit(x, default.units)
if(!is.unit(y)) y = unit(y, default.units)
if(!is.unit(w)) w = unit(w, default.units)
if(!is.unit(h)) h = unit(h, default.units)
if(!is.unit(l)) l = unit(l, default.units)
nx = length(x)
ny = length(y)
nw = length(w)
nh = length(h)
nl = length(l)
n = max(nx, ny, nw, nh, nl)
if(nx == 1) x = rep(x, n)
if(ny == 1) y = rep(y, n)
if(nw == 1) w = rep(w, n)
if(nh == 1) h = rep(h, n)
if(nl == 1) l = rep(l, n)
if(length(fill) == 1) fill = rep(fill, n)
if(any(theta < 0 | theta > 90)) {
stop_wrap("`theta` can only take value between 0 and 90.")
}
x1 = x - w*0.5
x2 = x + w*0.5
y1 = y - h*0.5
y2 = y + h*0.5
xu = x + l * cos(theta/180*pi)
yu = y + l * sin(theta/180*pi)
a1 = xu - w*0.5
a2 = xu + w*0.5
b1 = yu - h*0.5
b2 = yu + h*0.5
id = 1
px = NULL
py = NULL
pid = NULL
pfill = NULL
for(i in 1:n) {
fill2 = add_luminance(fill[i])
# front
if(is.null(px)) {
px = unit.c(x1[i], a1[i], a2[i], x2[i])
} else {
px = unit.c(px, x1[i], a1[i], a2[i], x2[i])
}
if(is.null(py)) {
py = unit.c(y1[i], b1[i], b1[i], y1[i])
} else {
py = unit.c(py, y1[i], b1[i], b1[i], y1[i])
}
pid = c(pid, rep(id, 4))
pfill = c(pfill, fill2[2])
id = id + 1
# left
px = unit.c(px, x1[i], x1[i], a1[i], a1[i])
py = unit.c(py, y1[i], y2[i], b2[i], b1[i])
pid = c(pid, rep(id, 4))
pfill = c(pfill, fill2[3])
id = id + 1
# top
px = unit.c(px, a1[i], a1[i], a2[i], a2[i])
py = unit.c(py, b1[i], b2[i], b2[i], b1[i])
pid = c(pid, rep(id, 4))
pfill = c(pfill, fill2[1])
id = id + 1
}
grid.polygon(px, py, id = pid, gp = gpar(fill = pfill, col = col))
}
# for a single color
add_luminance = function(col) {
rgb = col2rgb(col)
r = rgb[1, ]/255
g = rgb[2, ]/255
b = rgb[3, ]/255
col = as(RGB(r, g, b), "polarLUV")
value = coords(col)
sequential_hcl(
n = 9,
h = value[, "H"],
c = value[, "C"],
l = value[1, "L"]
)
}
# == title
# 3D Heatmap
#
# == param
# -matrix The input matrix. Values should be non-negative.
# -... All pass to `Heatmap`.
# -bar_rel_width A factor between 0 and 1.
# -bar_rel_height A factor between 0 and 1.
# -bar_max_length Maximal length of bars. Value should be in absolute unit.
# -bar_angle Angle for the projection.
# -row_names_side Row names are by default put on the left side of the heatmap.
# -show_row_dend By default the dendrogram is not drawn.
# -show_column_dend By default the dendrogram is not drawn.
#
# == detals
# For large matrices, the plotting might be slow.
#
# == example
# m = matrix(sample(100, 36), 6)
# Heatmap3D(m)
Heatmap3D = function(matrix,
...,
bar_rel_width = 0.6,
bar_rel_height = 0.6,
bar_max_length = unit(1, "cm"),
bar_angle = 60,
row_names_side = "left",
show_row_dend = FALSE,
show_column_dend = FALSE) {
if(any(matrix < 0)) {
stop_wrap("The matrix should be non-negative.")
}
if(bar_rel_width < 0 | bar_rel_width > 1) {
stop_wrap("`bar_rel_width` can only be set to a value between 0 and 1.")
}
if(bar_rel_height < 0 | bar_rel_height > 1) {
stop_wrap("`bar_rel_height` can only be set to a value between 0 and 1.")
}
ht = Heatmap(matrix, ..., rect_gp = gpar(type = "none"),
layer_fun = function(j, i, x, y, w, h, f) {
v = pindex(matrix, i, j)
od = rank(order(-as.numeric(y), -as.numeric(x)))
grid.rect(x[od], y[od], w[od], h[od], gp = gpar(col = "white", fill = "#EEEEEE"))
bar3D(x[od], y[od], w[od]*bar_rel_width, h[od]*bar_rel_height, v[od]/max(matrix)*bar_max_length, theta = bar_angle, fill = f[od])
},
show_row_dend = show_row_dend,
show_column_dend = show_column_dend,
row_names_side = row_names_side,
)
ht@heatmap_param$type = "Heatmap3D"
ht
}
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