Venn diagram using VennDiagram package

### Not to run ###

library(VennDiagram)

# peak names of metabolomes, filtered by different criteria
ever <- colnames(readRDS('data/metabolome_7080peaks.rds'))
incid <- colnames(readRDS('data/metabolome_7098peaks.rds'))
cur <- colnames(readRDS('data/metabolome_7109peaks.rds'))
onset <- colnames(readRDS('data/metabolome_7150peaks.rds'))
lc <- colnames(readRDS('data/metabolome_7300peaks.rds'))

# count each and every set and their intersection
n.ever <- length(ever)
n.incid <- length(incid)
n.cur <- length(cur)
n.onset <- length(onset)
n.lc <- length(lc)

n.ever.incid <- sum(ever %in% incid)
n.ever.cur <- sum(ever %in% cur)
n.ever.onset <- sum(ever %in% onset)
n.ever.lc <- sum(ever %in% lc)
n.incid.cur <- sum(incid %in% cur)
n.incid.onset <- sum(incid %in% onset)
n.incid.lc <- sum(incid %in% lc)
n.cur.onset <- sum(cur %in% onset)
n.cur.lc <- sum(cur %in% lc)
n.onset.lc <- sum(onset %in% lc)

n.ever.incid.cur <- sum(ever %in% incid & ever %in% cur)
n.ever.incid.onset <- sum(ever %in% incid & ever %in% onset)
n.ever.incid.lc <- sum(ever %in% incid & ever %in% lc)
n.ever.cur.onset <- sum(ever %in% cur & ever %in% onset)
n.ever.cur.lc <- sum(ever %in% cur & ever %in% lc)
n.ever.onset.lc <- sum(ever %in% onset & ever %in% lc)
n.incid.cur.onset <- sum(incid %in% cur & incid %in% onset)
n.incid.cur.lc <- sum(incid %in% cur & incid %in% lc)
n.incid.onset.lc <- sum(incid %in% onset & incid %in% lc)
n.cur.onset.lc <- sum(cur %in% onset & cur %in% lc)

n.ever.incid.cur.onset <- sum(ever %in% incid & ever %in% cur & ever %in% onset)
n.ever.incid.cur.lc <- sum(ever %in% incid & ever %in% cur & ever %in% lc)
n.ever.incid.onset.lc <- sum(ever %in% incid & ever %in% onset & ever %in% lc)
n.ever.cur.onset.lc <- sum(ever %in% cur & ever %in% onset & ever %in% lc)
n.incid.cur.onset.lc <- sum(incid %in% cur & incid %in% onset & incid %in% lc)

n.ever.incid.cur.onset.lc <-
  sum(ever %in% incid & ever %in% cur & ever %in% onset & ever %in% lc)

# venn diagram
png('results/descriptive_analyses/venn_diagram_5sets.png',
    height = 1600, width = 1600, res = 200)
draw.quintuple.venn(
  area1 = n.ever, area2 = n.incid, area3 = n.cur, area4 = n.onset, area5 = n.lc,
  n12 = n.ever.incid, n13 = n.ever.cur, n14 = n.ever.onset, n15 = n.ever.lc,
  n23 = n.incid.cur, n24 = n.incid.onset, n25 = n.incid.lc,
  n34 = n.cur.onset, n35 = n.cur.lc, n45 = n.onset.lc,
  n123 = n.ever.incid.cur, n124 = n.ever.incid.onset, n125 = n.ever.incid.lc,
  n134 = n.ever.cur.onset, n135 = n.ever.cur.lc, n145 = n.ever.onset.lc,
  n234 = n.incid.cur.onset, n235 = n.incid.cur.lc, n245 = n.incid.onset.lc,
  n345 = n.cur.onset.lc,
  n1234 = n.ever.incid.cur.onset, n1235 = n.ever.incid.cur.lc,
  n1245 = n.ever.incid.onset.lc, n1345 = n.ever.cur.onset.lc,
  n2345 = n.incid.cur.onset.lc, n12345 = n.ever.incid.cur.onset.lc,
  category = c('ever asthma', 'incident asthma', 'current asthma',
               'age of onset', 'LCA-derived classes'),
  lty = rep('blank', 5),
  fill = c('dodgerblue', 'goldenrod1', 'darkorange1', 'seagreen3', 'orchid3'),
  alpha = rep(0.5, 5), fontfamily = 'sans',
  cat.fontfamily = 'sans', scaled = FALSE,
  cat.pos = c(0,0,180,180,0), cat.dist = c(0.18, 0.2, 0.15, 0.17, 0.2))
dev.off()