When avg_type is added addtl_slider_stats reset to defaults

[Bernadetadad]

When avg_type is added to polyclonal_config.yaml it overrides all addtl_slider_stats and resets everything to altair defaults.

[jbloom]

@Bernadetadad, The issue is that you need to add the new key to the YAML dictionary, not overwrite it. This just has to do with how adding keys in YAML syntax via the merge operator works.

Consider this starting YAML file:

# overall default (contains some shared options)
overall_default: &overall_default
  min_epitope_activity_to_include: 0.2
  plot_kwargs:
    avg_type: median
    addtl_slider_stats:
      times_seen: 3
      functional effect: -4
    slider_binding_range_kwargs:
      n_models:
        step: 1
      times_seen:
        step: 1
        min: 1
        max: 25
    heatmap_max_at_least: 2
    heatmap_min_at_least: -2

# default configuration for monoclonal antibodies (mAbs)
mAb_default: &mAb_default
  <<: *overall_default
  max_epitopes: 1
  fit_kwargs:
    reg_escape_weight: 0.1
    reg_spread_weight: 0.25
    reg_activity_weight: 1.0

The mAb_default key is inheriting everything from overall_default (that is what <<: *overall_default means), and then it is adding to new keys for subdictionaries not defined in overall_default (these are max_epitopes and fit_kwargs).

Now consider if you do the following:

# overall default (contains some shared options)
overall_default: &overall_default
  min_epitope_activity_to_include: 0.2
  plot_kwargs:
    avg_type: median
    addtl_slider_stats:
      times_seen: 3
      functional effect: -4
    slider_binding_range_kwargs:
      n_models:
        step: 1
      times_seen:
        step: 1
        min: 1
        max: 25
    heatmap_max_at_least: 2
    heatmap_min_at_least: -2

# default configuration for monoclonal antibodies (mAbs)
mAb_default: &mAb_default
  <<: *overall_default
  plot_kwargs:
    avg_type: min_magnitude
  max_epitopes: 1
  fit_kwargs:
    reg_escape_weight: 0.1
    reg_spread_weight: 0.25
    reg_activity_weight: 1.0

What you may intend to do here is add a new values for the avg_type key to the plot_kwargs dictionary for mAb_default. But instead you are totally re-defining the plot_kwargs dictionary for mAb_default to only be {"plot_kwargs": {"avg_type": "min_magnitude"}}.

Instead what you need to do is this:

# default plot keyword arguments
default_plot_kwargs: &default_plot_kwargs
  avg_type: median
  addtl_slider_stats:
    times_seen: 3
    functional effect: -4
  slider_binding_range_kwargs:
    n_models:
      step: 1
    times_seen:
      step: 1
      min: 1
      max: 25
  heatmap_max_at_least: 2
  heatmap_min_at_least: -2

# overall default (contains some shared options)
overall_default: &overall_default
  min_epitope_activity_to_include: 0.2
  plot_kwargs:
    <<: *default_plot_kwargs

# default configuration for monoclonal antibodies (mAbs)
mAb_default: &mAb_default
  <<: *overall_default
  plot_kwargs:
    <<: *default_plot_kwargs
    avg_type: min_magnitude
  max_epitopes: 1
  fit_kwargs:
    reg_escape_weight: 0.1
    reg_spread_weight: 0.25
    reg_activity_weight: 1.0

I know it gets a bit complicated in syntax, but this is the best possible with YAML