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 :
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.
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.
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))
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nsetslimits the number of interactions shown to 7. If you want more than you have to increase that number.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
upsetfunction only and in the second code I usedfromListfunction as well. But results are different. I attached two figures (fromList and upset titles).upset and fromlist functions
Is
mydataa 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?