UpsetR intersection numbers

Question

[Mehmet]

Dear All,

I am using UpsetR for visualize OrthoFinder gene count results based on the command below:

upset(fromList(mydata), nsets = 7, matrix.color = "red", sets.bar.color = "blue")

This is my data:

   A B C  D E F  G
1  0 2 1  9 1 5 17
2  0 0 0  5 0 0  5
3  0 0 0  5 0 2 32
4  0 0 0 14 0 0 16
5  0 0 0  5 0 2 14
6  0 0 0  7 0 0  9
7  0 0 0 10 0 0  7
8  0 0 0 11 0 0  8
9  0 0 0  0 0 0  2
10 1 1 1  6 1 2  7
11 0 0 0  7 0 2  4
12 0 0 0  4 0 2  8
13 0 0 0  4 0 1 11
14 0 0 0  3 0 0  5
15 0 1 1  2 0 1  5
16 1 0 0  3 0 2  4
17 0 0 0  4 0 1  5
18 0 0 0  3 0 2  5
19 1 1 1  3 1 3  3
20 0 0 0  6 0 1  4

But I can not see the intersection of all columns. For instance at lines 10 and 19 there are numbers in all columns. But the figure does not have this. Am I missing something ?

The figure is at :

figure

[ATpoint]

nsets limits the number of interactions shown to 7. If you want more than you have to increase that number.

[Mehmet]

Thank you for reply, but it did not change.

I selected F and G columns only to test using two different functions below:

in the first code I used upset function only and in the second code I used fromList function as well. But results are different. I attached two figures (fromList and upset titles).

> upset(mydata, sets = c("F", "G"), matrix.color = "red", sets.bar.color = "blue",  nsets = 100000000000000000, group.by = "freq", order.by = "freq")

> upset(fromList(mydata), sets = c("F", "G"), matrix.color = "red", sets.bar.color = "blue",  nsets = 100000000000000000, group.by = "freq", order.by = "freq")

upset and fromlist functions

[igor]

Is mydata a list or a data frame? It should be a list. Based on the output, it looks like a data frame.

What does str(mydata) look like?

Answer 1

[Mehmet]

I converted mydata to a list as below:

> str(mydata)
List of 7
 $ A: int [1:99] 0 0 0 0 0 0 0 0 0 1 ...
 $ B: int [1:99] 2 0 0 0 0 0 0 0 0 1 ...
 $ C: int [1:99] 1 0 0 0 0 0 0 0 0 1 ...
 $ D: int [1:99] 9 5 5 14 5 7 10 11 0 6 ...
 $ E: int [1:99] 1 0 0 0 0 0 0 0 0 1 ...
 $ F: int [1:99] 5 0 2 0 2 0 0 0 0 2 ...
 $ G: int [1:99] 17 5 32 16 14 9 7 8 2 7 ...


> head(mydata)
$A
 [1] 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1
[53] 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 1 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

$B
 [1] 2 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1
[53] 0 1 0 0 0 1 1 1 1 1 1 1 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0

$C
 [1] 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1
[53] 0 1 0 0 0 0 0 2 1 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0

$D
 [1]  9  5  5 14  5  7 10 11  0  6  7  4  4  3  2  3  4  3  3  6  3  2  6  4  5  0  2  4  0  2  5  1  2  4
[35]  3  3  7  1  5  2  4  0  1  1  5  2  2  1  0  2  4  2  2  2  4  1  4  2  2  2  2  2  2  2  2  4  4  1
[69]  2  4  2  5  1  2  2  3  2  2  3  2  2  2  1  1  0  4  4  1  2  2  1  0  0  2  1  2  3  2  2

$E
 [1] 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1
[53] 1 1 0 0 0 0 0 2 1 1 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 1 1 2 0 0 0 0 0 0 0 0 0 2 0 0 0 1 0

$F
 [1]  5  0  2  0  2  0  0  0  0  2  2  2  1  0  1  2  1  2  3  1  2  2  8  2  1  0  1  1  0  0  1  1  1  6
[35]  0  2  0  1  2  2  0  0  0  0  2  2  1  2 16  2  1  2  1  2  0  1  1  2  1  2  1  2  2  1  2  1  1  0
[69]  1  1  1  0  4  1  2  2  0  2  1  1  1  1  1  2  0  0  0  0  2  0  0  2  3  0  1  0  0  1  1

and used as below:

> upset(mydata)
Error in 1:ncol(data) : argument of length 0

for another usage:

>upset(fromList(mydata), sets = c("A", "B"))

which shows the intersection size between A and B is 3, which is not true when I check the data.

[Mehmet]

OK.I have solved and I am explaining here.

UpsetR requires a binary data frame (numbers with zero and one only). Numbers bigger than 1 should replace with 1.The, upset function reads the data frame and produces graphs after calculating intersection size.

Probably, UpsetR ignores if a row is not consisted of binary data.

[igor]

UpsetR requires a binary data frame

UpsetR works with multiple data formats.

The vignette starts with a non-binary list as example:

# example of list input (list of named vectors)
listInput <- list(one = c(1, 2, 3, 5, 7, 8, 11, 12, 13), two = c(1, 2, 4, 5, 
    10), three = c(1, 5, 6, 7, 8, 9, 10, 12, 13))