output.txt

> library(UpSetR)

> library(org.Hs.eg.db)

> all_genes <- keys(org.Hs.eg.db)

> n_gene <- c(2000, 500, 1000, 900)

> # create a list, where each entry is the vector of Gene IDs that were diff
> # expressed in that condition
> # this is creating a random set of gene .... [TRUNCATED] 

> # give them names so we know what is what
> names(diff_genes) <- c("A", "B", "C", "D")

> # what does this look like? A list, where each one is a different set of genes
> str(diff_genes)
List of 4
 $ A: chr [1:2000] "728586" "406999" "56160" "105377483" ...
 $ B: chr [1:500] "54752" "389249" "101929386" "778" ...
 $ C: chr [1:1000] "399511" "342371" "347422" "66002" ...
 $ D: chr [1:900] "158800" "106480800" "51179" "105374729" ...

> length(intersect(diff_genes[[1]], diff_genes[[2]]))
[1] 18

> # use the fromList function to get it into the right shape
> compare_data <- fromList(diff_genes)

> # plot it!
> upset(compare_data)

upset_genediffs.R

library(UpSetR)
library(org.Hs.eg.db)

all_genes <- keys(org.Hs.eg.db)

n_gene <- c(2000, 500, 1000, 900)

# create a list, where each entry is the vector of Gene IDs that were diff
# expressed in that condition
# this is creating a random set of genes in each list entry
diff_genes <- lapply(n_gene, function(x){
  sample(all_genes, x)
})

# give them names so we know what is what
names(diff_genes) <- c("A", "B", "C", "D")

# what does this look like? A list, where each one is a different set of genes
str(diff_genes)

length(intersect(diff_genes[[1]], diff_genes[[2]]))

# use the fromList function to get it into the right shape
compare_data <- fromList(diff_genes)

# plot it!
upset(compare_data)