omarwagih/ggseqlogo

sequence logo with phosphorylated amino acids

Opened this issue · 3 comments

ryoshunki commented

Hello, I am using ggseqlogo to create a sequence logo from amino acids pwm, however, since my pwm also contain 3 phosphorylated amino acids phosphoserine, phosphothreonine and phosphotyrosine, it failed to create the right sequence logo with these 3 phopho amino acids(like this, there are some gaps which is supposed to be the positions of phospho amino acids). It would be so nice if somebody is going to help me.
image

omarwagih commented

Did you try the custom alphabets, see https://omarwagih.github.io/ggseqlogo/
Otherwise, can you post a reproducible example

ryoshunki commented

Oh I will try custom alphabets, thank you so much!!!

ryoshunki commented

I tried again and still can't make it,here is how my pwm looks like:
image
compared to usual pwm, information about phosphorylated amino acids is also included. So unlike usual 20 amino acids, pwm for 23 amino acids is included.
I will be so grateful if you can help me again