Chananchida Sang-aram

This is due to the behavior of `Seurat::AverageExpression` when using the `group.by` parameter (see [this issue](https://github.com/satijalab/seurat/issues/7893)).

- [ ] Add clearer documentation about 'scenario' and 'prioritizing weights' - [ ] Fix false warning

Warning message in `predict_ligand_activities`

3

When the regulatory potential of all genes in the gene set of interest is zero (for a certain ligand), this warning pops up: ``` Warning messages: 1: In evaluate_target_prediction(setting, ligand_target_matrix,...

* Change `p_val_x_adapted` to `p_val_adapted_x`, where x = "ligand" or "receptor". This mostly affects the `generate_prioritization_table` function. This data frame returned by this function now also has a "prioritization_rank" column...

The columns that are used to calculate cell type specificity are called `scaled_p_val_receptor_adapted` and `scaled_p_val_ligand_adapted` instead of having the `_ligand` and `_receptor` suffix at the end like other columns. This...