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mevers/my.vennDiagram.R

Last active August 27, 2020 08:42
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Modified limma::vennDiagram to remove box and add label
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my.vennDiagram.R
my.vennDiagram <- function (object, include = "both", names = NULL, mar = rep(1,
4), cex = c(1.5, 1, 0.7), lwd = 1, circle.col = NULL, counts.col = NULL,
show.include = NULL, ...)
{
include <- as.character(include)
LenInc <- min(length(include), 2)
if (is(object, "VennCounts")) {
include <- include[1]
LenInc <- 1
}
else {
if (LenInc > 1)
z2 <- vennCounts(object, include = include[2])[,
"Counts"]
object <- vennCounts(object, include = include[1])
}
z <- object[, "Counts"]
nsets <- ncol(object) - 1
if (nsets > 5)
stop("Can't plot Venn diagram for more than 5 sets")
VennZone <- object[, 1:nsets, drop = FALSE]
VennZone <- apply(VennZone, 1, function(x) paste(x, sep = "",
collapse = ""))
names(z) <- VennZone
if (length(include) == 2)
names(z2) <- VennZone
if (is.null(names))
names <- colnames(object)[1:nsets]
FILL.COL <- TRUE
if (is.null(circle.col)) {
circle.col <- par("col")
FILL.COL <- FALSE
}
if (length(circle.col) < nsets)
circle.col <- rep(circle.col, length.out = nsets)
if (is.null(counts.col))
counts.col <- par("col")
if (length(counts.col) < LenInc)
counts.col <- rep(counts.col, length.out = LenInc)
if (is.null(show.include))
show.include <- as.logical(LenInc - 1)
old.par <- par()$mar
on.exit(par(mar = old.par))
par(mar = mar)
if (nsets <= 3) {
plot(x = 0, y = 0, type = "n", xlim = c(-4, 4), ylim = c(-4,
4), xlab = "", ylab = "", axes = FALSE, ...)
theta <- 2 * pi * (0:360)/360
xcentres <- switch(nsets, 0, c(-1, 1), c(-1, 1, 0))
ycentres <- switch(nsets, 0, c(0, 0), c(1, 1, -2)/sqrt(3))
r <- 1.5
xtext <- switch(nsets, -1.2, c(-1.2, 1.2), c(-1.2, 1.2,
0))
ytext <- switch(nsets, 1.8, c(1.8, 1.8), c(2.4, 2.4,
-3))
for (circle in 1:nsets) {
if (!FILL.COL)
lines(xcentres[circle] + r * cos(theta), ycentres[circle] +
r * sin(theta), lwd = lwd, col = circle.col[circle])
if (FILL.COL) {
RGB <- col2rgb(circle.col[circle])/255
ALPHA <- 0.06
RGB.ALP <- rgb(RGB[1, 1], RGB[2, 1], RGB[3, 1],
alpha = ALPHA)
polygon(xcentres[circle] + r * cos(theta), ycentres[circle] +
r * sin(theta), border = circle.col[circle],
lwd = lwd, col = RGB.ALP)
}
text(xtext[circle], ytext[circle], names[circle],
cex = cex)
}
#switch(nsets, rect(-3, -2.5, 3, 2.5), rect(-3, -2.5,
# 3, 2.5), rect(-3, -3.5, 3, 3.3))
showCounts <- switch(nsets, function(counts, cex, adj,
col, leg) {
text(2.3, -2.1, sprintf("Not in any = %i", counts[1]), cex = cex, col = col,
adj = adj)
text(0, 0, counts[2], cex = cex, col = col, adj = adj)
if (show.include) text(-2.3, -2.1, leg, cex = cex,
col = col, adj = adj)
}, function(counts, cex, adj, col, leg) {
text(2.3, -2.1, sprintf("Not in any = %i", counts[1]), cex = cex, col = col,
adj = adj)
text(1.5, 0.1, counts[2], cex = cex, col = col, adj = adj)
text(-1.5, 0.1, counts[3], cex = cex, col = col,
adj = adj)
text(0, 0.1, counts[4], cex = cex, col = col, adj = adj)
if (show.include) text(-2.3, -2.1, leg, cex = cex,
col = col, adj = adj)
}, function(counts, cex, adj, col, leg) {
text(2.5, -3, sprintf("Not in any = %i", counts[1]), cex = cex, col = col, adj = adj)
text(0, -1.7, counts[2], cex = cex, col = col, adj = adj)
text(1.5, 1, counts[3], cex = cex, col = col, adj = adj)
text(0.75, -0.35, counts[4], cex = cex, col = col,
adj = adj)
text(-1.5, 1, counts[5], cex = cex, col = col, adj = adj)
text(-0.75, -0.35, counts[6], cex = cex, col = col,
adj = adj)
text(0, 0.9, counts[7], cex = cex, col = col, adj = adj)
text(0, 0, counts[8], cex = cex, col = col, adj = adj)
if (show.include) text(-2.5, -3, leg, cex = cex,
col = col, adj = adj)
})
if (LenInc == 1)
adj <- c(0.5, 0.5)
else adj <- c(0.5, 0)
print(z)
showCounts(counts = z, cex = cex[1], adj = adj, col = counts.col[1],
leg = include[1])
if (LenInc == 2)
showCounts(counts = z2, cex = cex[1], adj = c(0.5,
1), col = counts.col[2], leg = include[2])
return(invisible())
}
plot(c(-20, 420), c(-20, 420), type = "n", axes = FALSE,
ylab = "", xlab = "", ...)
relocate_elp <- function(e, alpha, x, y) {
phi <- (alpha/180) * pi
xr <- e[, 1] * cos(phi) + e[, 2] * sin(phi)
yr <- -e[, 1] * sin(phi) + e[, 2] * cos(phi)
xr <- x + xr
yr <- y + yr
cbind(xr, yr)
}
if (4 == nsets) {
#rect(-20, -20, 420, 400)
elps <- cbind(162 * cos(seq(0, 2 * pi, len = 1000)),
108 * sin(seq(0, 2 * pi, len = 1000)))
if (!FILL.COL) {
polygon(relocate_elp(elps, 45, 130, 170), border = circle.col[1],
lwd = lwd)
polygon(relocate_elp(elps, 45, 200, 200), border = circle.col[2],
lwd = lwd)
polygon(relocate_elp(elps, 135, 200, 200), border = circle.col[3],
lwd = lwd)
polygon(relocate_elp(elps, 135, 270, 170), border = circle.col[4],
lwd = lwd)
}
if (FILL.COL) {
RGB <- col2rgb(circle.col)/255
ALPHA <- 0.06
RGB.ALP1 <- rgb(RGB[1, 1], RGB[2, 1], RGB[3, 1],
alpha = ALPHA)
RGB.ALP2 <- rgb(RGB[1, 2], RGB[2, 2], RGB[3, 2],
alpha = ALPHA)
RGB.ALP3 <- rgb(RGB[1, 3], RGB[2, 3], RGB[3, 3],
alpha = ALPHA)
RGB.ALP4 <- rgb(RGB[1, 4], RGB[2, 4], RGB[3, 4],
alpha = ALPHA)
polygon(relocate_elp(elps, 45, 130, 170), border = circle.col[1],
lwd = lwd, col = RGB.ALP1)
polygon(relocate_elp(elps, 45, 200, 200), border = circle.col[2],
lwd = lwd, col = RGB.ALP2)
polygon(relocate_elp(elps, 135, 200, 200), border = circle.col[3],
lwd = lwd, col = RGB.ALP3)
polygon(relocate_elp(elps, 135, 270, 170), border = circle.col[4],
lwd = lwd, col = RGB.ALP4)
}
text(35, 315, names[1], cex = cex[1])
text(138, 350, names[2], cex = cex[1])
text(262, 347, names[3], cex = cex[1])
text(365, 315, names[4], cex = cex[1])
text(35, 250, z["1000"], cex = cex[2], col = counts.col[1],
)
text(140, 315, z["0100"], cex = cex[2], col = counts.col[1])
text(260, 315, z["0010"], cex = cex[2], col = counts.col[1])
text(365, 250, z["0001"], cex = cex[2], col = counts.col[1])
text(90, 282, z["1100"], cex = cex[3], col = counts.col[1])
text(95, 110, z["1010"], cex = cex[2], col = counts.col[1])
text(200, 52, z["1001"], cex = cex[3], col = counts.col[1])
text(200, 292, z["0110"], cex = cex[2], col = counts.col[1])
text(300, 110, z["0101"], cex = cex[2], col = counts.col[1])
text(310, 282, z["0011"], cex = cex[3], col = counts.col[1])
text(130, 230, z["1110"], cex = cex[2], col = counts.col[1])
text(245, 81, z["1101"], cex = cex[3], col = counts.col[1])
text(155, 81, z["1011"], cex = cex[3], col = counts.col[1])
text(270, 230, z["0111"], cex = cex[2], col = counts.col[1])
text(200, 152, z["1111"], cex = cex[2], col = counts.col[1])
text(400, 15, sprintf("Not in any = %i", z["0000"]), cex = cex[1], col = counts.col[1])
if (length(include) == 2) {
text(35, 238, z2["1000"], cex = cex[2], col = counts.col[2])
text(140, 304, z2["0100"], cex = cex[2], col = counts.col[2])
text(260, 304, z2["0010"], cex = cex[2], col = counts.col[2])
text(365, 238, z2["0001"], cex = cex[2], col = counts.col[2])
text(90, 274, z2["1100"], cex = cex[3], col = counts.col[2])
text(95, 100, z2["1010"], cex = cex[2], col = counts.col[2])
text(200, 43, z2["1001"], cex = cex[3], col = counts.col[2])
text(200, 280, z2["0110"], cex = cex[2], col = counts.col[2])
text(300, 100, z2["0101"], cex = cex[2], col = counts.col[2])
text(310, 274, z2["0011"], cex = cex[3], col = counts.col[2])
text(130, 219, z2["1110"], cex = cex[2], col = counts.col[2])
text(245, 71, z2["1101"], cex = cex[3], col = counts.col[2])
text(155, 72, z2["1011"], cex = cex[3], col = counts.col[2])
text(270, 219, z2["0111"], cex = cex[2], col = counts.col[2])
text(200, 140, z2["1111"], cex = cex[2], col = counts.col[2])
text(400, -2, sprintf("Not in any = %i", z2["0000"]), cex = cex[1], col = counts.col[2])
if (show.include) {
text(10, 15, include[1], cex = cex[1], col = counts.col[1])
text(10, -2, include[2], cex = cex[1], col = counts.col[2])
}
}
return(invisible())
}
#rect(-20, -30, 430, 430)
elps <- cbind(150 * cos(seq(0, 2 * pi, len = 1000)), 60 *
sin(seq(0, 2 * pi, len = 1000)))
if (!FILL.COL) {
polygon(relocate_elp(elps, 90, 200, 250), border = circle.col[1],
lwd = lwd)
polygon(relocate_elp(elps, 162, 250, 220), border = circle.col[2],
lwd = lwd)
polygon(relocate_elp(elps, 234, 250, 150), border = circle.col[3],
lwd = lwd)
polygon(relocate_elp(elps, 306, 180, 125), border = circle.col[4],
lwd = lwd)
polygon(relocate_elp(elps, 378, 145, 200), border = circle.col[5],
lwd = lwd)
}
if (FILL.COL) {
RGB <- col2rgb(circle.col)/255
ALPHA <- 0.06
RGB.ALP1 <- rgb(RGB[1, 1], RGB[2, 1], RGB[3, 1], alpha = ALPHA)
RGB.ALP2 <- rgb(RGB[1, 2], RGB[2, 2], RGB[3, 2], alpha = ALPHA)
RGB.ALP3 <- rgb(RGB[1, 3], RGB[2, 3], RGB[3, 3], alpha = ALPHA)
RGB.ALP4 <- rgb(RGB[1, 4], RGB[2, 4], RGB[3, 4], alpha = ALPHA)
RGB.ALP5 <- rgb(RGB[1, 5], RGB[2, 5], RGB[3, 5], alpha = ALPHA)
polygon(relocate_elp(elps, 90, 200, 250), border = circle.col[1],
lwd = lwd, col = RGB.ALP1)
polygon(relocate_elp(elps, 162, 250, 220), border = circle.col[2],
lwd = lwd, col = RGB.ALP2)
polygon(relocate_elp(elps, 234, 250, 150), border = circle.col[3],
lwd = lwd, col = RGB.ALP3)
polygon(relocate_elp(elps, 306, 180, 125), border = circle.col[4],
lwd = lwd, col = RGB.ALP4)
polygon(relocate_elp(elps, 378, 145, 200), border = circle.col[5],
lwd = lwd, col = RGB.ALP5)
}
text(50, 285, names[1], cex = cex[1])
text(200, 415, names[2], cex = cex[1])
text(350, 305, names[3], cex = cex[1])
text(350, 20, names[4], cex = cex[1])
text(100, -10, names[5], cex = cex[1])
text(61, 231, z["10000"], cex = cex[2], col = counts.col[1])
text(200, 332, z["01000"], cex = cex[2], col = counts.col[1])
text(321, 248, z["00100"], cex = cex[2], col = counts.col[1])
text(290, 84, z["00010"], cex = cex[2], col = counts.col[1])
text(132, 72, z["00001"], cex = cex[2], col = counts.col[1])
text(146, 253, z["11000"], cex = cex[3], col = counts.col[1])
text(123, 191, z["10100"], cex = cex[3], col = counts.col[1])
text(275, 155, z["10010"], cex = cex[3], col = counts.col[1])
text(137, 149, z["10001"], cex = cex[3], col = counts.col[1])
text(243, 271, z["01100"], cex = cex[3], col = counts.col[1])
text(175, 270, z["01010"], cex = cex[3], col = counts.col[1])
text(187, 120, z["01001"], cex = cex[3], col = counts.col[1])
text(286, 193, z["00110"], cex = cex[3], col = counts.col[1])
text(267, 238, z["00101"], cex = cex[3], col = counts.col[1])
text(228, 108, z["00011"], cex = cex[3], col = counts.col[1])
text(148, 213, z["11100"], cex = cex[3], col = counts.col[1])
text(159, 255, z["11010"], cex = cex[3], col = counts.col[1])
text(171, 144, z["11001"], cex = cex[3], col = counts.col[1])
text(281, 178, z["10110"], cex = cex[3], col = counts.col[1])
text(143, 166, z["10101"], cex = cex[3], col = counts.col[1])
text(252, 148, z["10011"], cex = cex[3], col = counts.col[1])
text(205, 258, z["01110"], cex = cex[3], col = counts.col[1])
text(254, 248, z["01101"], cex = cex[3], col = counts.col[1])
text(211, 121, z["01011"], cex = cex[3], col = counts.col[1])
text(267, 214, z["00111"], cex = cex[3], col = counts.col[1])
text(170, 234, z["11110"], cex = cex[3], col = counts.col[1])
text(158, 172, z["11101"], cex = cex[3], col = counts.col[1])
text(212, 142, z["11011"], cex = cex[3], col = counts.col[1])
text(263, 183, z["10111"], cex = cex[3], col = counts.col[1])
text(239, 235, z["01111"], cex = cex[3], col = counts.col[1])
text(204, 193, z["11111"], cex = cex[2], col = counts.col[1])
text(400, 7, sprintf("Not in any = %i", z["00000"]), cex = cex[1], col = counts.col[1])
if (length(include) == 2) {
text(61, 220, z2["10000"], cex = cex[2], col = counts.col[2])
text(200, 321, z2["01000"], cex = cex[2], col = counts.col[2])
text(321, 237, z2["00100"], cex = cex[2], col = counts.col[2])
text(290, 73, z2["00010"], cex = cex[2], col = counts.col[2])
text(132, 61, z2["00001"], cex = cex[2], col = counts.col[2])
text(146, 244, z2["11000"], cex = cex[3], col = counts.col[2])
text(123, 180, z2["10100"], cex = cex[3], col = counts.col[2])
text(275, 144, z2["10010"], cex = cex[3], col = counts.col[2])
text(137, 143, z2["10001"], cex = cex[3], col = counts.col[2])
text(243, 260, z2["01100"], cex = cex[3], col = counts.col[2])
text(175, 259, z2["01010"], cex = cex[3], col = counts.col[2])
text(187, 110, z2["01001"], cex = cex[3], col = counts.col[2])
text(286, 186, z2["00110"], cex = cex[3], col = counts.col[2])
text(267, 230, z2["00101"], cex = cex[3], col = counts.col[2])
text(228, 97, z2["00011"], cex = cex[3], col = counts.col[2])
text(148, 203, z2["11100"], cex = cex[3], col = counts.col[2])
text(159, 249, z2["11010"], cex = cex[3], col = counts.col[2])
text(171, 137, z2["11001"], cex = cex[3], col = counts.col[2])
text(281, 171, z2["10110"], cex = cex[3], col = counts.col[2])
text(143, 155, z2["10101"], cex = cex[3], col = counts.col[2])
text(252, 137, z2["10011"], cex = cex[3], col = counts.col[2])
text(205, 247, z2["01110"], cex = cex[3], col = counts.col[2])
text(254, 242, z2["01101"], cex = cex[3], col = counts.col[2])
text(211, 112, z2["01011"], cex = cex[3], col = counts.col[2])
text(267, 207, z2["00111"], cex = cex[3], col = counts.col[2])
text(170, 223, z2["11110"], cex = cex[3], col = counts.col[2])
text(158, 162, z2["11101"], cex = cex[3], col = counts.col[2])
text(212, 133, z2["11011"], cex = cex[3], col = counts.col[2])
text(263, 172, z2["10111"], cex = cex[3], col = counts.col[2])
text(239, 228, z2["01111"], cex = cex[3], col = counts.col[2])
text(204, 182, z2["11111"], cex = cex[2], col = counts.col[2])
text(400, -10, sprintf("Not in any = %i", z2["00000"]), cex = cex[1], col = counts.col[2])
if (show.include) {
text(10, 7, include[1], cex = cex[1], col = counts.col[1])
text(10, -10, include[2], cex = cex[1], col = counts.col[2])
}
}
invisible()
}
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