Diffbind plotting on contrasts
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Entering edit mode
medinaale • 0
@medinaale-7249
Last seen 6.7 years ago
Canada

Hi !

Hi

I want to draw a venn diagram of the peaks shared across four Tissues in my data set, but I'm not able to correctly select the set of peaks or create a contrast that achieves this.

The idea is to get four way vennDiagram with the four Tissues.

I have tried different things

> Example.data <- dba(sampleSheet=Example.table, minOverlap=1)
> Example.data.counts <- dba.count(Example.data, minOverlap=2,  score=score.value )
> Example.data.counts

8 Samples, 101978 sites in matrix:

       ID Tissue Factor Condition Replicate Caller Intervals FRiP

1 Tissue1_1  Tissue1     AC        EC         1 counts    101978 0.64

2 Tissue1_2  Tissue1     AC        EC         2 counts    101978 0.77

3 Tissue2_1  Tissue2 not_AC        EC         1 counts    101978 0.62

4 Tissue2_2  Tissue2 not_AC        EC         2 counts    101978 0.73

5  Tissue3_1   Tissue3 not_AC     NotEC         1 counts    101978 0.54

6  Tissue3_2   Tissue3 not_AC     NotEC         2 counts    101978 0.53

7 Tissue4_1  Tissue4 not_AC     NotEC         1 counts    101978 0.71

8 Tissue4_2  Tissue4 not_AC     NotEC         2 counts    101978 0.62

8 Samples, 101978 sites in matrix:

       ID Tissue Factor Condition Replicate Caller Intervals FRiP

1 Tissue1_1  Tissue1     AC        EC         1 counts    101978 0.64

2 Tissue1_2  Tissue1     AC        EC         2 counts    101978 0.77

3 Tissue2_1  Tissue2 not_AC        EC         1 counts    101978 0.62

4 Tissue2_2  Tissue2 not_AC        EC         2 counts    101978 0.73

5  Tissue3_1   Tissue3 not_AC     NotEC         1 counts    101978 0.54

6  Tissue3_2   Tissue3 not_AC     NotEC         2 counts    101978 0.53

7 Tissue4_1  Tissue4 not_AC     NotEC         1 counts    101978 0.71

8 Tissue4_2  Tissue4 not_AC     NotEC         2 counts    101978 0.62

> Example.data.counts.2 <- dba.contrast(Example.data.counts.2,categories=DBA_TISSUE, minMembers=2)


> Example.data.counts.2
8 Samples, 101978 sites in matrix:
       ID Tissue Factor Condition Replicate Caller Intervals FRiP
1 Tissue1_1  Tissue1     AC        EC         1 counts    101978 0.64
2 Tissue1_2  Tissue1     AC        EC         2 counts    101978 0.77
3 Tissue2_1  Tissue2 not_AC        EC         1 counts    101978 0.62
4 Tissue2_2  Tissue2 not_AC        EC         2 counts    101978 0.73
5  Tissue3_1   Tissue3 not_AC     NotEC         1 counts    101978 0.54
6  Tissue3_2   Tissue3 not_AC     NotEC         2 counts    101978 0.53
7 Tissue4_1  Tissue4 not_AC     NotEC         1 counts    101978 0.71
8 Tissue4_2  Tissue4 not_AC     NotEC         2 counts    101978 0.62

10 Contrasts:
   Group1 Members1 Group2 Members2
1   Tissue1        2  Tissue2        2
2   Tissue1        2   Tissue3        2
3   Tissue1        2  Tissue4        2
4   Tissue1        2 !Tissue1        6
5   Tissue2        2   Tissue3        2
6   Tissue2        2  Tissue4        2
7   Tissue2        2 !Tissue2        6
8    Tissue3        2  Tissue4        2
9    Tissue3        2  !Tissue3        6
10  Tissue4        2 !Tissue4        6


> dba.plotVenn(Example.data.counts.2, contrast=3)
Error in dba.plotVenn(Example.data.counts.2, contrast = 3) : 
  No peaksets meet specified criteria.
In addition: Warning message:
No valid contrasts/methods specified. 


I tried several contrast number and vectors and I never get a plot.

The I tried to do what is shown in the manual example:

> Example.data.counts.2 <- dba.peakset(Example.data.counts.2, consensus = DBA_TISSUE, minOverlap=0.66)
Add consensus: Tissue1
Add consensus: Tissue2
Add consensus: Tissue3
Add consensus: Tissue4
> dba.plotVenn(Example.data.counts.2, Example.data.counts.2$masks$Consensus)
Error in dba.plotVenn(Example.data.counts.2, Example.data.counts.2$masks$Consensus) : 
  Too many peaksets in mask.

Which makes sense since:
> Example.data.counts.2$masks$Consensus
Tissue1_1 Tissue1_2 Tissue2_1 Tissue2_2  Tissue3_1  Tissue3_2 Tissue4_1 Tissue4_2   Tissue1   Tissue2 
   TRUE    TRUE    TRUE    TRUE    TRUE    TRUE    TRUE    TRUE    TRUE    TRUE 
   Tissue3   Tissue4 
   TRUE    TRUE 

I thoguth that the idea of asking for the tissue consensus was to only get TRUEs in the last four terms since the other are the Replicate names.

Then I tried this:

dba.plotVenn(Example.data.counts.2, Example.data.counts.2$masks$Tissue1,Example.data.counts.2$masks$Tissue2,Example.data.counts.2$masks$Tissue3, Example.data.counts.2$masks$Tissue4 )

Now I don't get an error but I don't get a graph either.

If someone could provide some clues on how to achieve this I would really appreciate it.

diffbind chip-seq • 1.3k views
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0
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 3 days ago
CRUK, Cambridge, UK

Sorry it has taken a while to respond but I am travelling right now. I'll have to check later why the Consensus mask is all TRUE, but I can give you a workaround. Try:

dba.plotVenn(Example.data.counts.2, 9:12)

 

 

 

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Entering edit mode

I have looked into this further. in the development release (1,17) and onwards, dba,peakset() will abort with an error if you try to added consensus peaksets to what is already a consensus object after counting. dba.overlap() and dba.plotVenn() will, however, work if you want to see which of the peaks in the consensus were called in which sam

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