file to make UpSet plot of banana intersections

banana.R

# scraped from https://doi.org/10.1038/nature11241
# note that intersections < 100 not included
banana_sets <- c(
	Musa = 759,
	Phoenix = 769,
	Sorghum = 827,
	Brachypodium = 387,
	Ozyza = 1246,
	Arabidopsis = 1187,
	`Musa&Phoenix` = 467,
	`Brachypodium&Sorghum` = 402,
	`Musa&Brachypodium&Sorghum&Oryza` = 368,
	`Musa&Brachypodium&Sorghum&Oryza&Phoenix` = 685,
	`Brachypodium&Oryza` = 547,
	`Brachypodium&Sorghum&Oryza` = 2809,
	`Sorghum&Oryza` = 1151,
	`Brachypodium&Sorghum&Oryza&Phoenix` = 190,
	`Brachypodium&Sorghum&Oryza&Arabidopsis` = 206,
	`Musa&Brachypodium&Sorghum&Oryza&Arabidopsis` = 1458,
	`Musa&Brachypodium&Sorghum&Oryza&Phoenix&Arabidopsis` = 7674,
	`Phoenix&Brachypodium&Sorghum&Oryza&Arabidopsis` = 258,
	`Musa&Brachypodium&Sorghum&Phoenix&Arabidopsis` = 113,
	`Musa&Sorghum&Oryza&Phoenix&Arabidopsis` = 149,
	`Musa&Arabidopsis` = 155,
	`Musa&Phoenix&Arabidopsis` = 206,
	`Phoenix&Arabidopsis` = 105
	)

library(UpSetR)
bana_df <- fromExpression(banana_sets)

musa_list <- strsplit(grep("Musa",names(banana_sets[banana_sets>400]), value=TRUE), "&")
musa_list_plus <- lapply(musa_list, \(x) list(query = intersects, params = x, color = "gold", active=TRUE))
cols <- rep(c("grey30","gold","grey30"), c(3,1,2))

png(file="banana_upset.png", width=680, height=510, res=120)
upset(bana_df, nsets = 6, nintersects = 12, order.by = "freq",
      queries = musa_list_plus, sets.bar.color = cols)
dev.off()

Original

UpSet version