Upset plot mechanism

upsetwithlibrary.R

# Specific library
library(UpSetR)

# Dataset
input <- c(
  M.acuminata = 759,
  P.dactylifera = 769,
  A.thaliana = 1187,
  O.sativa = 1246,
  S.bicolor = 827,
  B.distachyon = 387,
  "P.dactylifera&M.acuminata" = 467,
  "O.sativa&M.acuminata" = 29,
  "A.thaliana&O.sativa" = 6,
  "S.bicolor&A.thaliana" = 9,
  "O.sativa&P.dactylifera" = 32,
  "S.bicolor&P.dactylifera" = 49,
  "S.bicolor&M.acuminata" = 49,
  "B.distachyon&O.sativa" = 547,
  "S.bicolor&O.sativa" = 1151,
  "B.distachyon&A.thaliana" = 10,
  "B.distachyon&M.acuminata" = 9,
  "B.distachyon&S.bicolor" = 402,
  "M.acuminata&A.thaliana" = 155,
  "A.thaliana&P.dactylifera" = 105,
  "B.distachyon&P.dactylifera" = 25,
  "S.bicolor&O.sativa&P.dactylifera" = 42,
  "B.distachyon&O.sativa&P.dactylifera" = 12,
  "S.bicolor&O.sativa&B.distachyon" = 2809,
  "B.distachyon&O.sativa&A.thaliana" = 18,
  "S.bicolor&O.sativa&A.thaliana" = 40,
  "S.bicolor&B.distachyon&A.thaliana" = 14,
  "O.sativa&B.distachyon&M.acuminata" = 28,
  "S.bicolor&B.distachyon&M.acuminata" = 13,
  "O.sativa&M.acuminata&P.dactylifera" = 35,
  "M.acuminata&S.bicolor&A.thaliana" = 21,
  "B.distachyon&M.acuminata&A.thaliana" = 7,
  "O.sativa&M.acuminata&A.thaliana" = 13,
  "M.acuminata&P.dactylifera&A.thaliana" = 206,
  "P.dactylifera&A.thaliana&S.bicolor" = 4,
  "O.sativa&A.thaliana&P.dactylifera" = 6,
  "S.bicolor&O.sativa&M.acuminata" = 64,
  "S.bicolor&M.acuminata&P.dactylifera" = 19,
  "B.distachyon&A.thaliana&P.dactylifera" = 3,
  "B.distachyon&M.acuminata&P.dactylifera" = 12,
  "B.distachyon&S.bicolor&P.dactylifera" = 23,
  "M.acuminata&B.distachyon&S.bicolor&A.thaliana" = 54,
  "P.dactylifera&S.bicolor&O.sativa&M.acuminata" = 62,
  "B.distachyon&O.sativa&M.acuminata&P.dactylifera" = 18,
  "S.bicolor&B.distachyon&O.sativa&A.thaliana" = 206,
  "B.distachyon&M.acuminata&O.sativa&A.thaliana" = 29,
  "O.sativa&M.acuminata&A.thaliana&S.bicolor" = 71,
  "M.acuminata&O.sativa&P.dactylifera&A.thaliana" = 28,
  "B.distachyon&M.acuminata&O.sativa&A.thaliana" = 7,
  "B.distachyon&S.bicolor&P.dactylifera&A.thaliana" = 11,
  "B.distachyon&O.sativa&P.dactylifera&A.thaliana" = 5,
  "A.thaliana&P.dactylifera&S.bicolor&O.sativa" = 21,
  "M.acuminata&S.bicolor&P.dactylifera&A.thaliana" = 23,
  "M.acuminata&B.distachyon&S.bicolor&P.dactylifera" = 24,
  "M.acuminata&O.sativa&S.bicolor&B.distachyon" = 368,
  "P.dactylifera&B.distachyon&S.bicolor&O.sativa" = 190,
  "P.dactylifera&B.distachyon&S.bicolor&O.sativa&A.thaliana" = 258,
  "P.dactylifera&M.acuminata&S.bicolor&B.distachyon&O.sativa" = 685,
  "M.acuminata&S.bicolor&B.distachyon&O.sativa&A.thaliana" = 1458,
  "S.bicolor&M.acuminata&P.dactylifera&O.sativa&A.thaliana" = 149,
  "B.distachyon&M.acuminata&P.dactylifera&O.sativa&A.thaliana" = 80,
  "M.acuminata&S.bicolor&B.distachyon&P.dactylifera&A.thaliana" = 113,
  "M.acuminata&S.bicolor&B.distachyon&P.dactylifera&O.sativa&A.thaliana" = 7674
)

# Plot
upset(fromExpression(input), 
      nintersects = 40, 
      nsets = 6, 
      order.by = "freq", 
      decreasing = T, 
      mb.ratio = c(0.6, 0.4),
      number.angles = 0, 
      text.scale = 1.1, 
      point.size = 2.8, 
      line.size = 1
)

upsetWithoutlibrary.R

values <- c(1:5)    
# define area for the histogram
par(fig=c(0.1,0.7,0.3,0.9))
barplot(values)
# define area for the boxplot
par(fig=c(0.8,1,0,1), new=TRUE)
stripchart(values, method="jitter")
# define area for the stripchart
par(fig=c(0.1,0.67,0.1,0.25), new=TRUE)
barplot(values, horiz = TRUE, axes=FALSE)
axis(1, at=-0:-8, labels=0:8)