I am trying to translate this bokeh alignment viewer into a plotly alignment viewer. I think for my purposes, this would work best with Plotly. I have been looking through the graphing library to figure out what the best way to get started would be. I have tried using a heatmap-like structure with text annotations but it does not seem very efficient. If anyone has any suggestions that would be greatly appreciated.
I do want to add that I have used the alignment chart in plotly but I just need more customizations so it just does not work for me.
Hi @Jeffy011 Could you share an image of what you want to achieve? Keep in mind that most here don’t know much about bokeh (me included).
I am so sorry. It seems that I forgot to link the alignment viewer I was trying to reference. Here is the code from Bokeh I was trying to follow: Bioinformatics and other bits - A sequence alignment viewer with Bokeh and Panel. Its essentially just a simple grid with one column for each amino acid. I tried doing something similar using heatmap and text but it was very slow. I appreciate the help.
HI @Jeffy011, looks interesting. Do you have some sample data?
A Scatterplot comes into my mind seeing this chart. This answer could be a starting point:
As far as I can see it, the color corresponds to the letter so you could map a unique color to each letter.
Yes thats exactly what it is. I will look at the code on the link provided and see if I could replicate it. I do have some sample data if you want to have a go at it. https://git.io/alignment_viewer_p53.fasta.
Please let me know if you would like me to provide more information.