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venn.5.by.prot.R
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venn.5.by.prot.R
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library(GenomicRanges)
library(data.table)
library(combinat)
library(VennDiagram)
rm(list = ls())
draw.quintuple.venn2 <- function (area1, area2, area3, area4, area5, n12, n13, n14, n15,
n23, n24, n25, n34, n35, n45, n123, n124, n125, n134, n135,
n145, n234, n235, n245, n345, n1234, n1235, n1245, n1345,
n2345, n12345, category = rep("", 5), lwd = rep(2, 5), lty = rep("solid",
5), col = rep("black", 5), fill = NULL, alpha = rep(0.5,
5), label.col = rep("black", 31), cex = rep(1, 31), fontface = rep("plain",
31), fontfamily = rep("serif", 31), cat.pos = c(0, 287.5,
215, 145, 70), cat.dist = rep(0.2, 5), cat.col = rep("black",
5), cat.cex = rep(1, 5), cat.fontface = rep("plain",
5), cat.fontfamily = rep("serif", 5), cat.just = rep(list(c(0.5,
0.5)), 5), rotation.degree = 0, rotation.centre = c(0.5,
0.5), ind = TRUE, cex.prop = NULL, print.mode = "raw",
sigdigs = 3, direct.area = FALSE, area.vector = 0, ...)
{
if (length(category) == 1) {
cat <- rep(category, 5)
}
else if (length(category) != 5) {
flog.error("Unexpected parameter length for 'category'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'category'")
}
if (length(lwd) == 1) {
lwd <- rep(lwd, 5)
}
else if (length(lwd) != 5) {
flog.error("Unexpected parameter length for 'lwd'", name = "VennDiagramLogger")
stop("Unexpected parameter length for 'lwd'")
}
if (length(lty) == 1) {
lty <- rep(lty, 5)
}
else if (length(lty) != 5) {
flog.error("Unexpected parameter length for 'lty'", name = "VennDiagramLogger")
stop("Unexpected parameter length for 'lty'")
}
if (length(col) == 1) {
col <- rep(col, 5)
}
else if (length(col) != 5) {
flog.error("Unexpected parameter length for 'col'", name = "VennDiagramLogger")
stop("Unexpected parameter length for 'col'")
}
if (length(label.col) == 1) {
label.col <- rep(label.col, 31)
}
else if (length(label.col) != 31) {
flog.error("Unexpected parameter length for 'label.col'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'label.col'")
}
if (length(cex) == 1) {
cex <- rep(cex, 31)
}
else if (length(cex) != 31) {
flog.error("Unexpected parameter length for 'cex'", name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cex'")
}
if (length(fontface) == 1) {
fontface <- rep(fontface, 31)
}
else if (length(fontface) != 31) {
flog.error("Unexpected parameter length for 'fontface'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'fontface'")
}
if (length(fontfamily) == 1) {
fontfamily <- rep(fontfamily, 31)
}
else if (length(fontfamily) != 31) {
flog.error("Unexpected parameter length for 'fontfamily'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'fontfamily'")
}
if (length(fill) == 1) {
fill <- rep(fill, 5)
}
else if (length(fill) != 5 & length(fill) != 0) {
flog.error("Unexpected parameter length for 'fill'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'fill'")
}
if (length(alpha) == 1) {
alpha <- rep(alpha, 5)
}
else if (length(alpha) != 5 & length(alpha) != 0) {
flog.error("Unexpected parameter length for 'alpha'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'alpha'")
}
if (length(cat.pos) == 1) {
cat.pos <- rep(cat.pos, 5)
}
else if (length(cat.pos) != 5) {
flog.error("Unexpected parameter length for 'cat.pos'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.pos'")
}
if (length(cat.dist) == 1) {
cat.dist <- rep(cat.dist, 5)
}
else if (length(cat.dist) != 5) {
flog.error("Unexpected parameter length for 'cat.dist'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.dist'")
}
if (length(cat.col) == 1) {
cat.col <- rep(cat.col, 5)
}
else if (length(cat.col) != 5) {
flog.error("Unexpected parameter length for 'cat.col'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.col'")
}
if (length(cat.cex) == 1) {
cat.cex <- rep(cat.cex, 5)
}
else if (length(cat.cex) != 5) {
flog.error("Unexpected parameter length for 'cat.cex'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.cex'")
}
if (length(cat.fontface) == 1) {
cat.fontface <- rep(cat.fontface, 5)
}
else if (length(cat.fontface) != 5) {
flog.error("Unexpected parameter length for 'cat.fontface'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.fontface'")
}
if (length(cat.fontfamily) == 1) {
cat.fontfamily <- rep(cat.fontfamily, 5)
}
else if (length(cat.fontfamily) != 5) {
flog.error("Unexpected parameter length for 'cat.fontfamily'",
name = "VennDiagramLogger")
stop("Unexpected parameter length for 'cat.fontfamily'")
}
if (!(class(cat.just) == "list" & length(cat.just) == 5 &
length(cat.just[[1]]) == 2 & length(cat.just[[2]]) ==
2 & length(cat.just[[3]]) == 2 & length(cat.just[[4]]) ==
2 & length(cat.just[[5]]) == 2)) {
flog.error("Unexpected parameter format for 'cat.just'",
name = "VennDiagramLogger")
stop("Unexpected parameter format for 'cat.just'")
}
cat.pos <- cat.pos + rotation.degree
if (direct.area) {
areas <- area.vector
for (i in 1:31) {
assign(paste("a", i, sep = ""), area.vector[i])
}
}
else {
a31 <- n12345
a30 <- n1234 - a31
a29 <- n1235 - a31
a28 <- n1245 - a31
a27 <- n1345 - a31
a26 <- n2345 - a31
a25 <- n245 - a26 - a28 - a31
a24 <- n234 - a26 - a30 - a31
a23 <- n134 - a27 - a30 - a31
a22 <- n123 - a29 - a30 - a31
a21 <- n235 - a26 - a29 - a31
a20 <- n125 - a28 - a29 - a31
a19 <- n124 - a28 - a30 - a31
a18 <- n145 - a27 - a28 - a31
a17 <- n135 - a27 - a29 - a31
a16 <- n345 - a26 - a27 - a31
a15 <- n45 - a18 - a25 - a16 - a28 - a27 - a26 - a31
a14 <- n24 - a19 - a24 - a25 - a30 - a28 - a26 - a31
a13 <- n34 - a16 - a23 - a24 - a26 - a27 - a30 - a31
a12 <- n13 - a17 - a22 - a23 - a27 - a29 - a30 - a31
a11 <- n23 - a21 - a22 - a24 - a26 - a29 - a30 - a31
a10 <- n25 - a20 - a21 - a25 - a26 - a28 - a29 - a31
a9 <- n12 - a19 - a20 - a22 - a28 - a29 - a30 - a31
a8 <- n14 - a18 - a19 - a23 - a27 - a28 - a30 - a31
a7 <- n15 - a17 - a18 - a20 - a27 - a28 - a29 - a31
a6 <- n35 - a16 - a17 - a21 - a26 - a27 - a29 - a31
a5 <- area5 - a6 - a7 - a15 - a16 - a17 - a18 - a25 -
a26 - a27 - a28 - a31 - a20 - a29 - a21 - a10
a4 <- area4 - a13 - a14 - a15 - a16 - a23 - a24 - a25 -
a26 - a27 - a28 - a31 - a18 - a19 - a8 - a30
a3 <- area3 - a21 - a11 - a12 - a13 - a29 - a22 - a23 -
a24 - a30 - a31 - a26 - a27 - a16 - a6 - a17
a2 <- area2 - a9 - a10 - a19 - a20 - a21 - a11 - a28 -
a29 - a31 - a22 - a30 - a26 - a25 - a24 - a14
a1 <- area1 - a7 - a8 - a18 - a17 - a19 - a9 - a27 -
a28 - a31 - a20 - a30 - a29 - a22 - a23 - a12
areas <- c(a1, a2, a3, a4, a5, a6, a7, a8, a9, a10, a11,
a12, a13, a14, a15, a16, a17, a18, a19, a20, a21,
a22, a23, a24, a25, a26, a27, a28, a29, a30, a31)
}
areas.error <- c("a1 <- area1 - a7 - a8 - a18 - a17 - a19 - a9 - a27 - a28 - a31 - a20 - a30 - a29 - a22 - a23 - a12",
"a2 <- area2 - a9 - a10 - a19 - a20 - a21 - a11 - a28 - a29 - a31 - a22 - a30 - a26 - a25 - a24 - a14",
"a3 <- area3 - a21 - a11 - a12 - a13 - a29 - a22 - a23 - a24 - a30 - a31 - a26 - a27 - a16 - a6 - a17",
"a4 <- area4 - a13 - a14 - a15 - a16 - a23 - a24 - a25 - a26 - a27 - a28 - a31 - a18 - a19 - a8 - a30",
"a5 <- area5 - a6 - a7 - a15 - a16 - a17 - a18 - a25 - a26 - a27 - a28 - a31 - a20 - a29 - a21 - a10",
"a6 <- n35 - a16 - a17 - a21 - a26 - a27 - a29 - a31",
"a7 <- n15 - a17 - a18 - a20 - a27 - a28 - a29 - a31",
"a8 <- n14 - a18 - a19 - a23 - a27 - a28 - a30 - a31",
"a9 <- n12 - a19 - a20 - a22 - a28 - a29 - a30 - a31",
"a10 <- n25 - a20 - a21 - a25 - a26 - a28 - a29 - a31",
"a11 <- n23 - a21 - a22 - a24 - a26 - a29 - a30 - a31",
"a12 <- n13 - a17 - a22 - a23 - a27 - a29 - a30 - a31",
"a13 <- n34 - a16 - a23 - a24 - a26 - a27 - a30 - a31",
"a14 <- n24 - a19 - a24 - a25 - a30 - a28 - a26 - a31",
"a15 <- n45 - a18 - a25 - a16 - a28 - a27 - a26 - a31",
"a16 <- n345 - a26 - a27 - a31", "a17 <- n135 - a27 - a29 - a31",
"a18 <- n145 - a27 - a28 - a31", "a19 <- n124 - a28 - a30 - a31",
"a20 <- n125 - a28 - a29 - a31", "a21 <- n235 - a26 - a29 - a31",
"a22 <- n123 - a29 - a30 - a31", "a23 <- n134 - a27 - a30 - a31",
"a24 <- n234 - a26 - a30 - a31", "a25 <- n245 - a26 - a28 - a31",
"a26 <- n2345 - a31", "a27 <- n1345 - a31", "a28 <- n1245 - a31",
"a29 <- n1235 - a31", "a30 <- n1234 - a31", "a31 <- n12345")
for (i in 1:length(areas)) {
if (areas[i] < 0) {
flog.error(paste("Impossible:", areas.error[i], "produces negative area"),
name = "VennDiagramLogger")
stop(paste("Impossible:", areas.error[i], "produces negative area"))
}
}
if (length(cex.prop) > 0) {
if (length(cex.prop) != 1)
flog.error("Value passed to cex.prop is not length 1",
name = "VennDiagramLogger")
stop("Value passed to cex.prop is not length 1")
func = cex.prop
if (class(cex.prop) != "function") {
if (cex.prop == "lin") {
func = function(x) x
}
else if (cex.prop == "log10") {
func = log10
}
else flog.error(paste0("Unknown value passed to cex.prop: ",
cex.prop), name = "VennDiagramLogger")
stop(paste0("Unknown value passed to cex.prop: ",
cex.prop))
}
maxArea = max(areas)
for (i in 1:length(areas)) {
cex[i] = cex[i] * func(areas[i])/func(maxArea)
if (cex[i] <= 0)
stop(paste0("Error in rescaling of area labels: the label of area ",
i, " is less than or equal to zero"))
}
}
grob.list <- gList()
dist <- 0.13
a <- 0.24
b <- 0.46
init.angle <- -20
ellipse.positions <- matrix(nrow = 5, ncol = 3)
colnames(ellipse.positions) <- c("x", "y", "rotation")
ellipse.positions[1, ] <- c(0.5 + dist * sin(init.angle *
pi/180), 0.5 + dist * cos(init.angle * pi/180), 0)
ellipse.positions[2, ] <- c(0.5 - dist * cos((288 + init.angle -
270) * pi/180), 0.5 + dist * sin((288 + init.angle -
270) * pi/180), -110)
ellipse.positions[3, ] <- c(0.5 - dist * sin((216 + init.angle -
180) * pi/180), 0.5 - dist * cos((216 + init.angle -
180) * pi/180), 145)
ellipse.positions[4, ] <- c(0.5 + dist * sin((180 - 144 -
init.angle) * pi/180), 0.5 - dist * cos((180 - 144 -
init.angle) * pi/180), 35)
ellipse.positions[5, ] <- c(0.5 + dist * cos((init.angle +
72 - 90) * pi/180), 0.5 - dist * sin((init.angle + 72 -
90) * pi/180), -72.5)
for (i in 1:5) {
grob.list <- gList(grob.list, VennDiagram::ellipse(x = ellipse.positions[i,
"x"], y = ellipse.positions[i, "y"], a = a, b = b,
rotation = ellipse.positions[i, "rotation"], gp = gpar(lty = 0,
fill = fill[i], alpha = alpha[i])))
}
for (i in 1:5) {
grob.list <- gList(grob.list, VennDiagram::ellipse(x = ellipse.positions[i,
"x"], y = ellipse.positions[i, "y"], a = a, b = b,
rotation = ellipse.positions[i, "rotation"], gp = gpar(lwd = lwd[i],
lty = lty[i], col = col[i], fill = "transparent")))
}
label.matrix <- matrix(nrow = 31, ncol = 3)
colnames(label.matrix) <- c("label", "x", "y")
label.matrix[1, ] <- c(a1, 0.4555, 0.9322)
label.matrix[2, ] <- c(a2, 0.08, 0.6)
label.matrix[3, ] <- c(a3, 0.3, 0.1)
label.matrix[4, ] <- c(a4, 0.79, 0.17)
label.matrix[5, ] <- c(a5, 0.9, 0.68)
label.matrix[6, ] <- c(a6, 0.74, 0.695)
label.matrix[7, ] <- c(a7, 0.63, 0.805)
label.matrix[8, ] <- c(a8, 0.4, 0.795)
label.matrix[9, ] <- c(a9, 0.255, 0.715)
label.matrix[10, ] <- c(a10, 0.193, 0.48)
label.matrix[11, ] <- c(a11, 0.225, 0.333)
label.matrix[12, ] <- c(a12, 0.42, 0.205)
label.matrix[13, ] <- c(a13, 0.572, 0.18)
label.matrix[14, ] <- c(a14, 0.753, 0.32)
label.matrix[15, ] <- c(a15, 0.823, 0.47)
label.matrix[16, ] <- c(a16, 0.747, 0.582)
label.matrix[17, ] <- c(a17, 0.662, 0.75)
label.matrix[18, ] <- c(a18, 0.488, 0.761)
label.matrix[19, ] <- c(a19, 0.323, 0.737)
label.matrix[20, ] <- c(a20, 0.253, 0.573)
label.matrix[21, ] <- c(a21, 0.225, 0.395)
label.matrix[22, ] <- c(a22, 0.355, 0.29)
label.matrix[23, ] <- c(a23, 0.515, 0.205)
label.matrix[24, ] <- c(a24, 0.655, 0.29)
label.matrix[25, ] <- c(a25, 0.783, 0.42)
label.matrix[26, ] <- c(a26, 0.72, 0.445)
label.matrix[27, ] <- c(a27, 0.605, 0.701)
label.matrix[28, ] <- c(a28, 0.342, 0.668)
label.matrix[29, ] <- c(a29, 0.294, 0.41)
label.matrix[30, ] <- c(a30, 0.522, 0.273)
label.matrix[31, ] <- c(a31, 0.5, 0.5)
processedLabels <- paste0(round(areas/119029689*100, digits = 2), "%")
if (print.mode[1] == "percent") {
processedLabels <- paste(round(label.matrix[, "label"]/119029689 * 100, digits = 2), "%", sep = "")
if (isTRUE(print.mode[2] == "raw")) {
processedLabels <- paste0(round(areas/119029689*100, digits = 2), "%")
}
}
if (print.mode[1] == "raw") {
processedLabels <- paste(round(label.matrix[, "label"]/119029689 * 100, digits = 2), "%", sep = "")
if (isTRUE(print.mode[2] == "percent")) {
processedLabels <- paste(processedLabels, "\\n(",
paste(round(label.matrix[, "label"]/119029689 * 100, digits = 2), "%", sep = ""),
sep = "")
}
}
for (i in 1:nrow(label.matrix)) {
tmp <- textGrob(label = processedLabels[i], x = label.matrix[i,
"x"], y = label.matrix[i, "y"], gp = gpar(col = label.col[i],
cex = cex[i], fontface = fontface[i], fontfamily = fontfamily[i]))
grob.list <- gList(grob.list, tmp)
}
cat.pos.x <- c(0.4555, 0.08, 0.3, 0.79, 0.9)
cat.pos.y <- c(0.9322, 0.6, 0.1, 0.17, 0.68)
for (i in 1:5) {
this.cat.pos <- find.cat.pos(x = cat.pos.x[i], y = cat.pos.y[i],
pos = cat.pos[i], dist = cat.dist[i])
grob.list <- gList(grob.list, textGrob(label = category[i],
x = this.cat.pos$x, y = this.cat.pos$y, just = cat.just[[i]],
gp = gpar(col = cat.col[i], cex = cat.cex[i], fontface = cat.fontface[i],
fontfamily = cat.fontfamily[i])))
}
grob.list <- VennDiagram::adjust.venn(VennDiagram::rotate.venn.degrees(grob.list,
rotation.degree, rotation.centre[1], rotation.centre[2]),
...)
if (ind) {
grid.draw(grob.list)
}
return(grob.list)
}
setwd(paste0("~/IMG/Projects/",
"HP1.Lamin.Polycomb.DNA.contacts.Effect.on.expression/",
"DamID-seq.HP1.PC.Lam.WBr.Nrn.Glia.Fb/21.07.17_1kbins_NRN/",
"sum_rep_qn/BioHMM2.qn.full.PC.HMM3/"))
euchr <- c("chr2L", "chr2R", "chr3L", "chr3R","chrX")
beds <- new.env()
for (i in dir()[grepl("bed", dir())]){
assign(sub("\\.domains.bed", "", i), fread(i, skip = 1), envir = beds)
}
rm(i)
prots <- unique(sub("[^.]+\\.([^.]+)", "\\1", names(beds)))
tiss <- unique(sub("^([^.]+)\\..*", "\\1", names(beds)))
tissnames <- c("Neurons", "Whole Brains", "Glia", "Kc167", "Fat Bodies")
comp_by_prot <- lapply(prots, function(prot){
retl <- list()
beds.p.i <- which(grepl(prot, names(beds)))
prots.grs <- lapply(beds.p.i, function(x){
df <- get(names(beds)[x], envir = beds)
names(df) <- c("chr", "start", "end")
df <- df %>% filter(chr %in% euchr)
GRanges(seqnames = Rle(df$chr),
ranges = IRanges(start = df$start, end = df$end))
})
names(prots.grs) <- sub("\\..+$", "", names(beds)[beds.p.i])
prots.grs <- prots.grs[order(names(prots.grs))]
# Length of plain domains
prots.grs.wid <- sapply(prots.grs, function(lst) sum(width(lst)))
names(prots.grs.wid) <- names(prots.grs)
retl[["dom.1x.width"]] <- prots.grs.wid
# Width of all 2x intersects
prots.grs.by2 <- combn(prots.grs, 2, simplify = F)
prots.gr.width.by2 <- sapply(prots.grs.by2, function(lst){
intrsct <- Reduce(GenomicRanges::intersect, lst)
sum(width(reduce(intrsct)))
})
twb.names <- sapply(prots.grs.by2, function(comb){
Reduce(function(x,y) paste(x, y, sep=".vs."), names(comb))
})
names(prots.gr.width.by2) <- twb.names
retl[["int.dom.2x"]] <- (prots.gr.width.by2)
# Width of all 3x intersects
prots.grs.by3 <- combn(prots.grs, 3, simplify = F)
prots.gr.width.by3 <- sapply(prots.grs.by3, function(lst){
intrsct <- Reduce(GenomicRanges::intersect, lst)
sum(width(reduce(intrsct)))
})
twb.names <- sapply(prots.grs.by3, function(comb){
Reduce(function(x,y) paste(x, y, sep=".vs."), names(comb))
})
names(prots.gr.width.by3) <- twb.names
retl[["int.dom.3x"]] <- (prots.gr.width.by3)
# Width of all 4x intersects
prots.grs.by4 <- combn(prots.grs, 4, simplify = F)
prots.gr.width.by4 <- sapply(prots.grs.by4, function(lst){
intrsct <- Reduce(GenomicRanges::intersect, lst)
sum(width(reduce(intrsct)))
})
twb.names <- sapply(prots.grs.by4, function(comb){
Reduce(function(x,y) paste(x, y, sep=".vs."), names(comb))
})
names(prots.gr.width.by4) <- twb.names
retl[["int.dom.4x"]] <- (prots.gr.width.by4)
# Width of 5x intersect
tot.intrsct <- Reduce(GenomicRanges::intersect, prots.grs)
retl[["int.dom.5x"]] <- sum(width(reduce(tot.intrsct)))
# anti-domains
prots.gaps <- lapply(prots.grs, gaps)
gaps.intrsct <- Reduce(GenomicRanges::intersect, prots.gaps)
retl[["antidomains.width"]] <- sum(width(reduce(gaps.intrsct)))
return(retl)
})
names(comp_by_prot) <- prots
venn.plot <- draw.quintuple.venn2(mode = "percent",
area1 = comp_by_prot[[2]][[1]][[1]],
area2 = comp_by_prot[[2]][[1]][[2]],
area3 = comp_by_prot[[2]][[1]][[3]],
area4 = comp_by_prot[[2]][[1]][[4]],
area5 = comp_by_prot[[2]][[1]][[5]],
n12 = comp_by_prot[[2]][[2]][[1]],
n13 = comp_by_prot[[2]][[2]][[2]],
n14 = comp_by_prot[[2]][[2]][[3]],
n15 = comp_by_prot[[2]][[2]][[4]],
n23 = comp_by_prot[[2]][[2]][[5]],
n24 = comp_by_prot[[2]][[2]][[6]],
n25 = comp_by_prot[[2]][[2]][[7]],
n34 = comp_by_prot[[2]][[2]][[8]],
n35 = comp_by_prot[[2]][[2]][[9]],
n45 = comp_by_prot[[2]][[2]][[10]],
n123 = comp_by_prot[[2]][[3]][[1]],
n124 = comp_by_prot[[2]][[3]][[2]],
n125 = comp_by_prot[[2]][[3]][[3]],
n134 = comp_by_prot[[2]][[3]][[4]],
n135 = comp_by_prot[[2]][[3]][[5]],
n145 = comp_by_prot[[2]][[3]][[6]],
n234 = comp_by_prot[[2]][[3]][[7]],
n235 = comp_by_prot[[2]][[3]][[8]],
n245 = comp_by_prot[[2]][[3]][[9]],
n345 = comp_by_prot[[2]][[3]][[10]],
n1234 = comp_by_prot[[2]][[4]][[1]],
n1235 = comp_by_prot[[2]][[4]][[2]],
n1245 = comp_by_prot[[2]][[4]][[3]],
n1345 = comp_by_prot[[2]][[4]][[4]],
n2345 = comp_by_prot[[2]][[4]][[5]],
n12345 = comp_by_prot[[2]][[5]],
category = c(paste0("Whole Brains\n", round(comp_by_prot[[2]][[1]][[1]]/119029689*100, digits = 2), "%"),
paste0("Fat bodies\n", round(comp_by_prot[[2]][[1]][[2]]/119029689*100, digits = 2), "%"),
paste0("Glia\n", round(comp_by_prot[[2]][[1]][[3]]/119029689*100, digits = 2), "%"),
paste0("Kc167\n", round(comp_by_prot[[2]][[1]][[4]]/119029689*100, digits = 2), "%"),
paste0("Neurons\n", round(comp_by_prot[[2]][[1]][[5]]/119029689*100, digits = 2), "%")),
fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
cat.cex = 2,
margin = 0.1,
ind = TRUE
)
grid.text(paste0("Non-domains:\n",
round(comp_by_prot[[2]][[6]]/119029689*100, digits = 2),
"%"),
x = unit(0.9, "npc"), y = unit(0.9, "npc"),
just = "centre", hjust = NULL, vjust = NULL, rot = 0,
check.overlap = FALSE, default.units = "npc",
name = NULL, gp = gpar(fontfamily = "serif", fontsize = 20, fontface = "plain"), draw = TRUE, vp = NULL)
pdf("hp1.venn.5tiss.pdf", width = 10, height = 8)
print(venn.plot)
dev.off()