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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog.

6.12

  • Switch to using scipy.sparse arrays rather than matrices to keep up with this change to binarymap (now require binarymap >= 0.7).
  • Remove pin on urllib3

6.11

  • In lineplot_and_heatmap, add mean_abs and sum_abs as possible site statistics, reflecting the mean and sum of the absolute values of the mutation values.

6.10

  • In lineplot_and_heatmap, mutations that are hidden are by one slider filtered even if they fail other sliders. Addresses this issue

6.9

  • Added rename_std option to lineplot_and_heatmaps, which fixes a quasi-bug introduced in the rename_stat_col option by the changes in version 6.8.

6.8

  • Add addtl_slider_stats_as_max to lineplot_and_heatmap.
  • Show escape_std in PolyclonalCollection.mut_escape_plot and PolyclonalCollectios.mut_icXX_plot

6.7

  • Add heatmap_lims_from_slider_init option to lineplot_and_heatmap so that by default heatmap range is set by data shown with initial slider stats. Set this option to False if you want old behavior for plot limits
  • Set default init_floor_at_zero for mut_icXX_plot to be True like for other plots.
  • Ensure that wildtype identity is always shown in heatmap tooltips even if mutation is filtered.

6.6

  • Change lineplot_and_heatmap parameter addtl_slider_stats_hide_not_filter (which is used to make the escape heatmaps) so that mutations that have null escape but a non-null but hidden value are shown as grayed out (hidden) rather than missing. The use case is so that deleterious mutations that don't have escape measured but fail the functional effects filter are shown grayed out to indicate that they were measured and are deleterious, rather than leaving them out which implies they were not measured.
  • Fix bug where scale_stat_col to per-model values in tooltips when using PolyclonalCollection.mut_escape_plot and PolyclonalCollections.mut_escape_icXX.
  • Add min_times_seen filter to PolyclonalCollection.mut_escape_corr and PolyclonalCollection.mut_escape_corr_heatmap.

6.5

  • Fix bug in Polyclonal.icXX when the ICXX is at the bounds.
  • Increase the range of min_c, max_c, and check_wt_icXX in mut_icXX-related methods.

6.4

  • Fixed bug introduced in version 6.3 in PolyclonalCollection.sites when sites are integer.

6.3

  • Ensure PolyclonalCollection.sites attribute is always defined.
  • Move testing from Travis to GitHub actions.

6.2

  • Correctly implement change in icXX intended in version 6.1.

6.1

  • Increase range of concentrations accepted by icXX methods.

6.0

  • Upgrade minimum altair to 5.0.0
  • Use ruff as linter rather than flake8
  • Add Polyclonal.mut_icXX_df method
  • Add Polyclonal.mut_icXX_plot method
  • Add PolyclonalCollection.mut_icXX_df_replicates, PolyclonalCollection.mut_icXX_df, and PolyclonalCollection.mut_icXX_df_w_model_values methods.
  • Add PolyclonalCollection.mut_icXX_plot method

5.3

  • Add min_escape_magnitude as an option for PolyclonalAverage escape averages and plots. This gives the value across models with the lowest magnitude (smallest absolute value).

5.2

  • In polyclonal.plot.lineplot_and_heatmap, apply any hiding filter sliders before doing the max of the stat at the site slider. This avoids showing sites with all hidden values when trying to look at max.
  • Pass nbval tests with pandas 2.0.

5.1

  • Update to using altair version 5.0.0rc1, which can be installed by pip. This also means for the first time polyclonal itself can be on PyPI, which changes installation instructions.

5.0

  • Increase default reg_activity_weight from 1.0 to 2.0, note that this will change results relative to models fit with earlier versions with the old default weight.
  • Improvements to fitting of models: - The optimization bounds to Polyclonal.fit can now be set as parameters (activity_bounds, etc) rather than hard-coded. - Change regularization on Hill coefficient to a more quadratic form. - Adjust regularization weight for Hill coefficient (decreasing to 25) - Put upper bound on non-neutralizable fraction of 0.5. - Add (and activate by default) fit_fixed_first to fit a model with a fixed Hill coefficient and non-neutralized fraction first, and the fit_fixed_first_reg_activity_weight option to fit it with a higher weight.
  • Add check_concentration_scale to Polyclonal to keep concentrations in data to fit in reasonable range.

4.1

  • Added sites_to_show option to polyclonal.plot.lineplot_and_heatmap.
  • Remove is_weighted_replicate from curves_plot tooltip (it was an error this was ever shown).

4.0

  • Enable (and activate by default) fitting of a Hill coefficient and non-neutralized fraction in the curves. Previously, the Hill coefficient had been constrained to one and the non-neutralized fraction to zero. This is a major change that will alter the results of fitting models. To get the old behavior, call Polyclonal.fit with fix_hill_coefficient=True and fix_non_neutralized_frac=True. Specific changes associated with this update include: - Add hill_coefficient_df and non_neutralized_frac_df as parameters and properties of Polyclonal and PolyclonalCollection. - Restructure internal organization of Polyclonal._params (this was private, so external code should not be using anyway). - Add regularization to Hill coefficient and non-neutralized fraction to Polyclonal.fit. - Add the "two-epitope" example to illustrate the non-one Hill coefficient and non-neutralized fractions not equal to zero.
  • Update reg_escape_weight to 0.05 in Polyclonal.fit because it seems like many people in lab were using larger values. This will change results of fitting models because old default was 0.02.
  • Add the curves_plot and curve_specs_df to Polyclonal / PolyclonalCollection, curves_plot to the plots module, and prefer use of this over the activity barplots in the docs. The reason is that this shows the activity, Hill coefficient, and non-neutralized frac.
  • Remove bootstrapping from docs as this isn't really a recommended procedure.
  • Updated the default colors for epitopes (changing fourth to light blue and adding olive as fifth)

3.4

  • Plotting improvements:
  • Add heatmap_max_fixed and heatmap_min_fixed to plot.lineplot_and_heatmap
  • Make it easier to access per-model measurements for averages of models:
  • added PolyclonalCollection.unique_descriptor_names attribute.
  • added PolyclonalCollection.mut_escape_df_model_values property
  • added per_model_tooltip option to PolyclonalCollection.mut_escape_plot, and make this the default when <=5 models.
  • Heatmap tooltips now show missing (null) numerical values as NaN rather than as 0.
  • Update altair version to commit to f8912bad75d4247ab726b639968b13315161660a (note that the latest version still not merged on altair main branch, so still having to install from GitHub). In this new version, alt.add_parameter becomes alt.add_params and alt.parameter becomes alt.param.
  • Implemented slider that hides rather than filters mutations on the heatmaps. This is designed for mutation effect filtering where we'd like to be able to see which mutations have poor effects. They are now filtered from lineplot calculation and shown as gray. Adds the following parameters to plot.lineplot_and_heatmap:
  • addtl_slider_stats_hide_not_filter
  • hide_color
  • also very slight changes to colors in background of heatmap.
  • Re-order default positive color scheme to put green before dark byzantium to give better clarity relative to hidden / filtered values in heatmaps.
  • Updated notebooks to use new plotting.

3.3

  • Add options for lineplot only or heatmap only in plot.lineplot_and_heatmap (these are show_zoombar, show_lineplot, and show_heatmap).
  • Add scale_stat_col option to plot.lineplot_and_heatmap.
  • Add rename_stat_col option to plot.lineplot_and_heatmap.

3.2

  • Allow non-integer PDB numbers in B-factor re-assignment in reassign_b_factor.

3.1

  • Change default positive colors.

3.0

  • Make Polyclonal.spatial_distances a public attribute.
  • Polyclonal.fit allows epitopes with identical activities if they have different escape.
  • Activity regularization penalizes both positive and negative values.
  • Checks and int versus str dtype adjustment for spatial_distances in Polyclonal.
  • Adjust activity regularization based on concentration geometric mean so it is not sensitive to units of concentration.
  • Renamed what was previously called the epitope similarity regularization to epitope uniqueness-squared, as it's a second uniqueness regularization but operates on square of escape values.
  • Change default regularization strengths in Polyclonal.fit.
  • Rename reg_spatial_weight2 to reg_spatial2_weight for Polyclonal.fit.
  • Update default values of regularization weights.
  • Added antibody cocktail and HIV serum examples.
  • Updated examples, for instance by adding spatial regularization to RBD example and slightly changing simulated data.

2.6

  • Flatten mutation-escape values for RBD simulation so most values are roughly zero. Previously many values were ~0.5 rather than 0. Also adjust activities for this simulation.
  • Improve column spacing when Polyclonal.fit prints log.
  • Added 'atom' as output column in pdb_utils.extract_atom_locations
  • Added pdb_utils.inter_residue_distances
  • Added Polyclonal.distance_matrix attribute, set via spatial_distances parameter.
  • Added spatial regularization to Polyclonal.fit
  • Added uniqueness regularization to Polyclonal.fit as an alternative to similarity regularization that does not go with square of site-level values.

2.5

  • Add epitope similarity regularization that can be tuned by the parameter reg_similarity_weight.
  • Add real_mAb_cocktail.ipynb notebook that fits model to a real mAb cocktail dataset.

2.4

  • Fix bug introduced in version 2.3 that dropped wildtype sites if there were minimums set in slider_binding_range_kwargs to lineplot_and_heatmap.

2.3

  • lineplot_and_heatmap computes the limit for the heatmap range after applying the minimum filters specified in the filters. This avoids having the range determined by mutations that are never plotted, and so is sort of a bug fix (prior behavior wasn't strictly a bug, but did not give sensible behavior).

2.2

  • Require at least pandas 1.5.
  • Some minor changes to avoid pandas warnings about future deprecations.
  • For Polyclonal initialization, allow data_mut_escape_overlap != "exact" even with sites set

2.1

  • lineplot_and_heatmap filters site max value after other slider filters, this gives correct behavior and is sort of a bug fix for the plots.
  • Add slider_binding_range_kwargs to lineplot_and_heatmap
  • Allow df_to_merge to be list for mut_escape_plot methods.

2.0

Many of these changes are backward incompatible with respect to plotting.

  • Changed plotting of escape. Replaced mut_escape_heatmap and mut_escape_lineplot with lineplot_and_heatmap
  • Changed default epitope colors for Polyclonal objects.
  • Replaced Polyclonal.mut_escape_heatmap and Polyclonal.mut_escape_lineplot with Polyclonal.mut_escape_plot.
  • Replaced PolyclonalCollection.mut_escape_heatmap and PolyclonalCollection.mut_escape_lineplot with PolyclonalCollection.mut_escape_plot.

1.2

  • PolyclonalCollection plotting (specifically lineplot) still works even if there is just one model in collection. Before this edge case caused an error.
  • Allow negative site numbers.

1.1

  • Sort sites in mutation and site-escape data frames output by PolyclonalCollection.

1.0

  • Renamed the bootstrapping models from PolyclonalCollection to PolyclonalBootstrap and made PolyclonalCollection a general-purpose class for collection of Polyclonal objects. This makes the idea of model collections more general, and better aligns the class names with what they actually do. This is a backward-incompatible change.
  • Added methods for correlating models to PolyclonalCollection: methods mut_escape_corr, mut_escape_corr_heatmap.
  • Added sites parameter to Polyclonal to enable non-sequential-integer (eg, reference) based site numbering, and propagated this change to plotting and PolyclonalCollection.
  • Added the PolyclonalAverage class for computing the average of models.
  • PolyclonalCollection and subclasses return both mean and median and provide option to plot either, and PolyclonalCollection.default_avg_to_plot attribute added.
  • Remove the old Polyclonal.harmonize_epitopes_with method that modified Polyclonal models in place, and replaced with the new Polyclonal.epitope_harmonized_model that returns a copy of the original model with the epitopes harmonized and also provides guarantees about consistent epitope order, etc. This is a backward-incompatible change.
  • Added alphabets.biochem_order_aas and by default plot heatmaps with biochemically ordered amino acids.
  • Added n_replicates slider to PolyclonalCollection.mut_escape_heatmap
  • Added min_replicates to PolyclonalCollection.mut_escape_lineplot
  • Added plot.corr_heatmap function.
  • Added utils.tidy_to_corr function.
  • Added polyclonal_collection.fit_models to fit multiple models using multiprocessing.
  • Added RBD_average.ipynb notebook.
  • Fix bug in setting epitope_colors as dict in Polyclonal.
  • Fix SettingWithCopyWarning in heatmap plotting.
  • Added letter_suffixed_sites parameter to MutationParser and site_level_variants.
  • Added sites to plot.mut_escape_heatmap and plot.mut_escape_lineplot to enable ordering of str site numbers and utilized within Polyclonal objects.
  • Increment binarymap version requirement to >= 0.5.
  • Changed real antibody example from REGN10933 to LY-CoV1404

0.3

  • Add some options that generalize mut_escape_heatmap, specifically: * allow wildtype entries to be specified (with effects of 0) in mut_escape_df. This helps allow additional tooltips. * added max_min_times_seen and some tweaks to times seen tooltip * added addtl_sliders_stats

0.2

  • Add some options that generalize mut_escape_heatmap, specifically: * added epitope_label_suffix parameter * added diverging_colors parameter * changed percent_max_cutoff slider to work on real rather than absolute values and with non-zero minimum values.

0.1

Initial release