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dms-vep / dms-vep-pipeline

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Option to display by the smaller escape value #153

Closed Bernadetadad closed 1 year ago

Bernadetadad commented 1 year ago

@jbloom I think it would actually be nice to have an option to display the smaller of the two replicate escape values on the heatmaps. Maybe this could be added to .config as an option in addition of median/mean that are available now.

jbloom commented 1 year ago

Can be addressed after polyclonal 5.3 version is created with this change: https://github.com/jbloomlab/polyclonal/pull/163

jbloom commented 1 year ago

@Bernadetadad, This will be enabled in version 2.5.0, which should be available shortly.

You can set avg_type: min_magnitude under plot_kwargs in the polyclonal_config.yaml file, and that will display the escape value with the minimum overall magnitude (absolute value) across models for each mutation.

Bernadetadad commented 1 year ago

@jbloom min_magnitude only works if replicates have escape values that are both either positive or both negative but not if one value is negative and the other is positive.

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jbloom commented 1 year ago

@Bernadetadad, it actually does work here: in this case, it is showing the value with the lowest magnitude. That is why it is called min_magnitude.

Do you want me to also implement an option called min that just returns the absolute minimum? I can do that, but keep in mind that if you then have values like -0.1 and -5.3, it will return -5.3.

jbloom commented 1 year ago

@Bernadetadad, I just wanted to re-up this. Is the explanation above satisfactory and I can close this issue, or did you have some other statistic in mind to calculate and if so what?

Bernadetadad commented 1 year ago

yes, I'm closing it.