upsetR plots

Venn diagrams blow. 
Multiset Venn diagrams both blow and suck:

• Don't make them;
•  and don't make me interpret them;
•  and don't try and put them in your presentations because you'll get lost

UpSetR provides a way to do the multi-set comparison thing without looking horrific.

We sample a few sets from the letters `b-z`:

library("UpSetR")

set.seed(1)

bucket_names <- paste0("set", 1:6)

buckets <- Map(
  function(x){
    bucket_size <- sample(1:25, 1)
    bucket <- sample(letters[-1], bucket_size, replace = FALSE)
    },
  bucket_names
  )

lapply(buckets, sort)
$set1
[1] "f" "k" "n" "o" "t" "v" "x"

$set2
 [1] "c" "d" "f" "h" "i" "j" "k" "m" "n" "o" "q" "r" "s" "w" "y" "z"

$set3
 [1] "b" "e" "i" "k" "l" "m" "p" "v" "x" "y"

$set4
 [1] "b" "c" "d" "f" "g" "i" "k" "l" "n" "o" "p" "q" "s" "t" "u" "v" "w" "x" "y"
[20] "z"

$set5
 [1] "c" "f" "h" "j" "k" "n" "q" "r" "s" "t" "v" "w" "y"

$set6
 [1] "b" "c" "d" "e" "f" "g" "i" "j" "k" "l" "m" "n" "p" "q" "r" "s" "t" "u" "w"
[20] "x" "z"

The function `upset` takes a dataframe as input. But I've just defined my sets as a list of vectors. To convert these into a dataframe, use `UpSetR::fromList`:

fromList(buckets)

   set1 set2 set3 set4 set5 set6

1     1    1    1    1    1    1

2     1    1    0    1    0    0

3     1    0    1    1    1    0

4     1    1    0    1    1    1

5     1    0    0    1    1    1

6     1    0    1    1    0    1

7     1    1    0    1    1    1

8     0    1    0    1    1    1

9     0    1    1    1    1    0

10    0    1    0    1    1    1

11    0    1    0    0    1    1

12    0    1    0    1    1    1

13    0    1    0    0    1    1

14    0    1    0    0    1    0

15    0    1    1    0    0    1

16    0    1    0    1    0    1

17    0    1    1    1    0    1

18    0    1    0    1    0    1

19    0    1    0    1    1    1

20    0    0    1    1    0    1

21    0    0    1    1    0    1

22    0    0    1    0    0    1

23    0    0    1    1    0    1

24    0    0    0    1    0    1

25    0    0    0    1    0    1

The letter 'a' is absent from every one of these sets. you could add a `universe` entry or a `unobserved` entry to the set-list passed to `fromList` if that's what you're into.

Otherwise, to generate an upset plot do the following:

upset(
  fromList(buckets)

  )

This gives the following plot:

We note a couple of things: 

• `set1` is absent from the image, although it contained 7 elements;
• the elements of a given set are partitioned between the bars: eg, `set3` contains 9 elements, that are split over the 4-5th, 8-9th and 12-14th columns (the numbers above these columns add up to 9) so each element in set3 is put into a single column
• that means, although the intersection between set3 and set6 is of size 8, there is only one element in the "set3 and set6" intersection column (the remaining 6 are partitioned across the other columns that contain both set3 and set6)

To ensure that all the sets are displayed in the figure, modify the `nsets` argument:

You can order the bars by size (`order.by = "freq"`) or by the number of sets that contributed to the intersection (`order.by = "degree"`) or by both:

# order by freq
upset(
  fromList(buckets), nsets = length(buckets), order.by = "freq"

)

# order by degree and then by freq (not shown)
upset(
  fromList(buckets), order.by = c("freq", "degree"),
  nsets = length(buckets)
  )
# order by freq and then by degree (not shown)
upset(
  fromList(buckets), order.by = c("degree", "freq"),
  nsets = length(buckets)

  )

I found the latter a bit weird, in that order.by = c("degree", "freq") sorts by increasing frequency, whereas order.by="freq" sorts by decreasing frequency.

That'll do