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Glitch or Feature? Either methods do not represent the true distribution of an allele when gaps are involved
Hello! I use ggseqlogo to produce logoplots for HIV variants. I recently have come across an inconsistency that I have questions about.
Here is an explanation to the issue I have: In Donor#X, a Gap in site 26 is not reflected on the logoplot. ggseqlogo shows a gap in that site only if all the sequences in that position have a gap. Or else it gives a 100% probability to an allele even if it's present in just one sequence. This was seen in both
Here is an Image I have attached of the logoplot and the consensus matrix. Please see sites 26 and 27.
The A at 26 is full sized even though it is present only in 1 sequence out of 18 total sequences. The rest of them have a "-".
Similarly, I expected site 27s G to be a little smaller due to the fact that it was seen only in 17/18 sequences.
I got the same results even with the "Bits" method.
![Screenshot 2023-03-14 at 2 03 10 AM](https://user-images.githubusercontent.com/123095463/224910247-9182f0ce-e49d-41a7-8f5f-1afa2e8f9da7.png)
Can you share example data for me to be able to fully reproduce?
I have included the aligned fasta sequences and my consensus matrix and logolot for reference.
Hello! Just following up to see if there are any insights to this issue.