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)
)
- `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
