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dms-vep / LASV_Josiah_GP_DMS

Analysis of DMS data on Lassa virus GP using dms-vep-pipeline-3
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remove gaps from alphabet when plotting heat maps #4

Closed jbloom closed 10 months ago

jbloom commented 10 months ago

Gaps are essentially not present in your libraries.

You can pass alphabet to the plotting via plot_kwargs for both antibody escape and functional effects (https://jbloomlab.github.io/polyclonal/_modules/polyclonal/plot.html#lineplot_and_heatmap).

I would recommend setting an alphabet that just has the 21 non-stop characters (the amino acids and a stop codon), and not including a gap.

Caleb-Carr commented 10 months ago

I'm closing the above issue with the following edits made:

  1. A 21 character alphabet consisting of the 20 amino acids and stop codon was added for both functional and antibody selection heatmaps with the following commit 22e442442072475bd6d5c7d555deedc7c9a29e7d

Note: The use of a stop codon character ("*") needs to be correctly double escaped depending on aliasing in the data/func_effects_config.yml and data/antibody_escape_config.yml files