- Initial release of the
configure_dms_vizproject.
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- Make it possible to choose the colors on the negative color scale for each condition.
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- Make it possible to choose the colors on the negative color scale for each condition.
- Fixed a bug where the filter columns were used for both filter and tooltip columns regardless of user input.
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- Fixed a bug that occurs if
NaNvalues are found in themetriccolumn. IfNaNis present the visualization tool records these is 'observed' but 'filtered' due to the wayNaNvalues are handled by the visualization. There is no reason to have measurements withNaNin the metric column, so these are filtered out and the user is warned about their presence.
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- Added tests/examples for three new datasets:
- Caelan's HIV DMS data
- Jesse's SARS-CoV-2 mutation fitness data
- The Lauring lab's IAV PB1 DMS data
- Configured the tests with
pytest
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- Add SARS-CoV-2 RBD antibody escape example
- Filter out sites that don't have any mutations
- Updated the descriptions for each test/example
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- Add a subcommand that joins together datasets into a single JSON file.
- Breaking change that splits configure-dms-viz into to subcommads – format and join.
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- Add the ability to include a 'chain' column in the sitemap to support discontinuous sites.
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- Add the ability to specify a default value for the filter sliders.
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- It's now possible to include
protein_sitesproceed by insertion codes like (i.e. 52A, 214B, etc...). Previously,protein_sitescould only be numeric and non-numeric sites were ignored by thedms-viz.
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- Added a warning to
joinif twojsondatasets have the name top-level key/name.
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- Don't allow white space or empty strings for included/excluded chains.
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- Sitemaps are now optional. If you do not provide one, all sites are sequential and the reference sites in your input data are the same as the protein sites.
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- When checking the protein structure, don't include site with non-matching wildtype resides as "missing".
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- Fix a bug where
proteinsites aren't properly mapped to the structure if they're of typeFloat.
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- Throw an error if the same chains are present in
includedandexcludedchain lists
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- Fixes a bug where the markdown description was included in the count of keys compared to the number of input files causing the join command to exit before completing.
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- Added a flag (--heatmap-limits) to allow users to set the limits of the color scale.
- Added a human dataset (PTEN VAMPseq)
- Attempt to sort the reference sites when no sitemap is provided
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- Added a flag (--summary-stat) to allow users to set the default summary metric
- Added a flag (--floor) to allow users to set whether the data is floor by default
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- Sort the keys in the output JSON to prevent overhead in
gitdiffs.
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