Align Notation

[wes-lewis]

This PR aligns LOCAT code naming with manuscript notation and clarifies depletion vs concentration semantics across the codebase.

Summary
Renamed depletion-scan API and variables to manuscript-style terms.
Renamed key output fields for clarity and consistency.
Updated downstream plotting code to consume new field names.
Standardized expression matrix access naming (W) in LOCAT classes.
Kept behavior unchanged; this is primarily a naming/consistency refactor.
Key changes

1. Depletion scan naming aligned to manuscript
   In both locat/locat_condensed.py and locat/locat_condensed_git.py:

localization_pval_dep_scan -> depletion_pval_scan
c_values -> lambda_values
loop variable c -> lambda_
rc_c_values -> rc_lambda_values
best_c -> best_lambda
per_c -> per_lambda
n_eff -> n_eff_g
n_trials -> n_trials_eff
This makes depletion threshold notation match manuscript
λ
λ-based notation and distinguishes gene-specific effective sample size.

2. Output key updates
   n_components -> K_components (matches manuscript
   K
   g
   K
   g
   ​
   )
   added/used depletion_pval for depletion score output
   added/used h_size and h_sens for final-score penalty terms
   diagnostics key uses depletion_scan
3. LOCAT data matrix naming
   Introduced/used W property in LOCAT classes for expression matrix access (matching manuscript
   W
   W).
4. Downstream caller updates
   In locat/plotting_and_other_methods.py:

switched plot annotations from localization_pval to depletion_pval
updated labels accordingly (DepPval, dep_pval)
Validation
python -m py_compile passes for:
locat/locat_condensed.py
locat/locat_condensed_git.py
locat/plotting_and_other_methods.py
Notes
Refactor is intended to improve naming consistency and interpretability.
Functional/statistical behavior is unchanged; only identifiers/field names were aligned.

[fra-pcmgf]

Looks good!