Change prioritization table and mushroom plot defaults

[csangara]

• 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 that contains the rankings of the LR pairs based on "prioritization_score" (with rank 1 being the highest).

The behavior of make_mushroom_plot function is also changed as follows:

• Default color is now the "scaled_p_val_adapted" column instead of "scaled_lfc" to better evaluate cell type specificity criteria (as the lfc column wasn't used for prioritization anyway)
• Sender cell types (x-axis) now follows the order of prioritization_table$sender column if it is a factor
• size parameter is checked for the correct range (between 0 and 1.001) to prevent overgrown mushrooms
• Addition of a new parameter called use_absolute_rank (default: FALSE) that will determine whether the absolute rankings are used to filter the table to top_n. If TRUE, this may return an empty table for cell types where LR pairs are all ranked lowly.
• (Not relevant for users) Added keywords for this column (as p-value was written as "p_val" instead of "pval" unlike the other columns)