Nothing
plotVenn3d <-
function(x, labels = c('A','B','C'),
Colors = c("red","yellow","orange","lightblue","purple","green","grey"),
Title = NULL, shrink=1, rot=0)
{ # plot a 3-dimensional Venn diagram
# suppressPackageStartupMessages(library(grid))
### Specify necessary functions
getArcEnds <- function(center1, center2, radius)
{
calcdist <- function(x,y) sqrt((x[1] - y[1])^2 + (x[2] - y[2])^2)
calcangle <- function(x,y) atan((y[2] - x[2]) / (y[1] - x[1]))
centerDistance <- calcdist(center1, center2)
connector <- ifelse(center1[1] > center2[1], pi, 0) + calcangle(center1, center2)
intersection <- acos((centerDistance / 2) / radius)
c(begin=connector - intersection, end=connector + intersection)
}
arcPoints <- function(beginpt, endpt, center, radius)
{
angles <- seq(beginpt, endpt, length=nfacets)
x <- center[1] + radius * cos(angles)
y <- center[2] + radius * sin(angles)
list(x=x,y=y)
}
getArc <- function(center1, center2, radius)
{
ends <- getArcEnds(center1, center2, radius)
arcPoints(ends["begin"], ends["end"], center1, radius)
}
twoWayOverlap <- function(center1, center2, radius, color)
{
points1 <- getArc(center1, center2, radius)
points2 <- getArc(center2, center1, radius)
points <- list()
points$x <- c(points1$x,points2$x)
points$y <- c(points1$y,points2$y)
grid.polygon(x=points$x, y=points$y, gp=gpar(fill=color))
}
centralArcs <- function(centers, i, radius)
{
if (i == 1) { j <- 2; k <- 3}
if (i == 2) { j <- 1; k <- 3}
if (i == 3) { j <- 2; k <- 1}
endsone <- getArcEnds(centers[[i]], centers[[j]], radius)
endstwo <- getArcEnds(centers[[i]], centers[[k]], radius)
if (endsone[2] < 0) endsone <- endsone + 2 * pi
if (endstwo[2] < 0) endstwo <- endstwo + 2 * pi
if (endstwo[1] < endsone[1] & endsone[1] < endstwo[2]) {
return (arcPoints(endsone[1], endstwo[2], centers[[i]], radius))
} else {
return (arcPoints(endstwo[1], endsone[2], centers[[i]], radius))
}
}
fromBase2 <- function(x) 4 * as.numeric(substr(x,1,1)) + 2 * as.numeric(substr(x,2,2)) + as.numeric(substr(x,3,3))
rotateCoordinates <- function(xy, tiltpi)
{
if (is.null(nrow(xy))) adjustCenter <- plotCenter
else adjustCenter <- matrix(rep(plotCenter,nrow(xy)), byrow=TRUE, nrow=nrow(xy))
rotationMatrix <- matrix(c(cos(tiltpi), -sin(tiltpi), sin(tiltpi), cos(tiltpi)), byrow=TRUE, ncol=2)
(xy - adjustCenter) %*% rotationMatrix + adjustCenter
}
### Initialize variables
rot <- rot %% 360
tiltpi <- rot * pi / 180
if (missing(x)) x <- paste(seq(15), Colors)
values <- rep(0, length(x))
if (is.null(names(x)))
names(x) <- c("101","110","010","001","011","100","111")[seq(length(x))]
valptr <- unlist(lapply(names(x), fromBase2))
inputColors <- Colors
for (i in seq_along(x))
if (valptr[i] %in% 1:7) {
values[valptr[i]] <- values[valptr[i]] + x[i]
Colors[valptr[i]] <- inputColors[i]
}
nfacets <- 300
radius <- 0.25
r0 <- .18
dy <- r0 * sin(pi/6)
dx <- r0 * cos(pi/6)
labx0 <- .29
labx1 <- 1.5
labx2 <- .75
plotCenter <- c(0.5, ifelse(is.null(Title),.5, .43))
centers <- list(
c(plotCenter[1], plotCenter[2] + r0),
c(plotCenter[1] - dx, plotCenter[2] - dy),
c(plotCenter[1] + dx, plotCenter[2] - dy))
angle <- seq(0, 2*pi, length=nfacets) [-nfacets]
points1 <- centralArcs(centers, 1, radius)
points2 <- centralArcs(centers, 2, radius)
points3 <- centralArcs(centers, 3, radius)
points <- list()
points$x <- c(points1$x, points2$x, points3$x)
points$y <- c(points1$y, points2$y, points3$y)
if (tiltpi != 0) {
pointsxy <- rotateCoordinates(cbind(points$x, points$y), tiltpi)
points$x <- pointsxy[,1]
points$y <- pointsxy[,2]
centers <- sapply(centers, function(x) list(rotateCoordinates(x, tiltpi)))
}
### label and region-center locations
labelLocations <- rotateCoordinates(matrix(c(
plotCenter[1], plotCenter[2] + r0 + labx0,
plotCenter[1] - dx, plotCenter[2] - dy - labx0,
plotCenter[1] + dx, plotCenter[2] - dy - labx0
), byrow=TRUE, ncol=2), tiltpi)
centerLocations <- rotateCoordinates(matrix(c(
plotCenter[1] + dx * labx1, plotCenter[2] - dy * labx1,
plotCenter[1] - dx * labx1, plotCenter[2] - dy * labx1,
plotCenter[1], plotCenter[2] - r0 * labx2,
plotCenter[1], plotCenter[2] + r0 * labx1,
plotCenter[1] + dx * labx2, plotCenter[2] + dy * labx2,
plotCenter[1] - dx * labx2, plotCenter[2] + dy * labx2,
plotCenter[1], plotCenter[2]
), byrow=TRUE, ncol=2), tiltpi)
### Plot
if (!is.null(Title))
grid.text(Title, gp = gpar(fontsize=25*shrink, fontface="bold"),x = plotCenter[1], y = 0.97)
grid.polygon(x=centers[[1]][1] + radius*cos(angle), y=centers[[1]][2] + radius*sin(angle), gp=gpar(fill=Colors[4]))
grid.polygon(x=centers[[2]][1] + radius*cos(angle), y=centers[[2]][2] + radius*sin(angle), gp=gpar(fill=Colors[2]))
grid.polygon(x=centers[[3]][1] + radius*cos(angle), y=centers[[3]][2] + radius*sin(angle), gp=gpar(fill=Colors[1]))
twoWayOverlap(centers[[1]], centers[[2]], radius, Colors[6])
twoWayOverlap(centers[[2]], centers[[3]], radius, Colors[3])
twoWayOverlap(centers[[1]], centers[[3]], radius, Colors[5])
grid.polygon(x=points$x, y=points$y, gp=gpar(fill=Colors[7]))
for (i in 1:3) grid.text(labels[i], labelLocations[i,1], labelLocations[i,2], gp = gpar(fontsize=18*shrink, fontface="bold"))
for (i in 1:7) grid.text(values[i], centerLocations[i,1], centerLocations[i,2])
}
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