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jbloomlab / phydms

phylogenetic analyses informed by deep mutational scanning data
GNU General Public License v3.0
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phydms_plotselection #39

Closed Hamil462 closed 4 years ago

Hamil462 commented 4 years ago

Hi, I am trying to run an analysis using phydms_plotselection after phydms but this program does not seem to be present in the repository, so I keep getting "no such file or directory" errors even after importing. Where can I access this code? Thanks.

skhilton commented 4 years ago

Thanks for your interest in phydms!

phydms_plotselection is not a phydms function. You can use phydms to create logoplots using the script phydms_logoplot with documentation here. Alternatively, the package dmslogo is a more flexible tool for logoplots. If you provide me an example of the type of plot you are trying to create or recreate I might be able to provide more help!

Hamil462 commented 4 years ago

Hi, Thanks for replying! phydms_plotselection definitely used to be a function as it was used by Jesse Bloom in the notebook found at https://github.com/jbloomlab/AtlasPaper_SUMO1_UBE2I_ExpCM/blob/master/SUMO_and_UBE2I_analysis.ipynb to plot sites with strong selective bias (the plots near the bottom of the page). I know that the logoplots are useful for plotting amino acid frequency, but what might you suggest to represent selection if plotselection is no longer available?

From: Sarah Hilton notifications@github.com Sent: Thursday, September 17, 2020 11:47 AM To: jbloomlab/phydms phydms@noreply.github.com Cc: Rayna Hamilton hamilt43@myumanitoba.ca; Author author@noreply.github.com Subject: Re: [jbloomlab/phydms] phydms_plotselection (#39)

Thanks for your interest in phydms!

phydms_plotselection is not a phydms function. You can use phydms to create logoplots using the script phydms_logoplot with documentation herehttp://jbloomlab.github.io/phydms/phydms_logoplot.html. Alternatively, the package dmslogohttps://jbloomlab.github.io/dmslogo/index.html is a more flexible tool for logoplots. If you provide me an example of the type of plot you are trying to create or recreate I might be able to provide more help!

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jbloom commented 4 years ago

It was in version 1., but is not part of version 2.. If you want to use it, install version 1.*. Note however that we are no longer supporting that version.