Use the information from the niche- and spatial differential expression analysis of ligand-senders and receptor-receivers pairs, in addition to the ligand activity prediction and ligand-target inferernce, in order to make a final ligand-receptor and ligand-target prioritization table.

get_prioritization_tables Use the information from the niche- and spatial differential expression analysis of ligand-senders and receptor-receivers pairs, in addition to the ligand activity prediction and ligand-target inferernce, in order to make a final ligand-receptor and ligand-target prioritization table.

Usage

get_prioritization_tables(output_nichenet_analysis, prioritizing_weights)

Arguments

output_nichenet_analysis: List containing following data frames: DE_sender_receiver, ligand_scaled_receptor_expression_fraction_df, sender_spatial_DE_processed, receiver_spatial_DE_processed, ligand_activities_targets, DE_receiver_processed_targets, exprs_tbl_ligand, exprs_tbl_receptor, exprs_tbl_target
prioritizing_weights: Named numeric vector in the form of: #' prioritizing_weights = c("scaled_ligand_score" = 5,

Value

A list containing a prioritization table for ligand-receptor interactions, and one for ligand-target interactions

Examples

if (FALSE) { # \dontrun{
prioritizing_weights <- c(
  "scaled_ligand_score" = 5,
  "scaled_ligand_expression_scaled" = 1,
  "ligand_fraction" = 1,
  "scaled_ligand_score_spatial" = 2,
  "scaled_receptor_score" = 0.5,
  "scaled_receptor_expression_scaled" = 0.5,
  "receptor_fraction" = 1,
  "ligand_scaled_receptor_expression_fraction" = 1,
  "scaled_receptor_score_spatial" = 0,
  "scaled_activity" = 0,
  "scaled_activity_normalized" = 1
)
output_nichenet_analysis <- list(
  DE_sender_receiver = DE_sender_receiver, ligand_scaled_receptor_expression_fraction_df = ligand_scaled_receptor_expression_fraction_df, sender_spatial_DE_processed = sender_spatial_DE_processed, receiver_spatial_DE_processed = receiver_spatial_DE_processed,
  ligand_activities_targets = ligand_activities_targets, DE_receiver_processed_targets = DE_receiver_processed_targets, exprs_tbl_ligand = exprs_tbl_ligand, exprs_tbl_receptor = exprs_tbl_receptor, exprs_tbl_target = exprs_tbl_target
)
prioritization_tables <- get_prioritization_tables(output_nichenet_analysis, prioritizing_weights)
} # }