R/ligand_receptor.R

In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

annotate_ligand_receptor_interactions <- function(qgenes,
                                                  genedb = NULL,
                                                  ligand_receptor_db = NULL,
                                                  ligand_receptor_xref = NULL) {

  lgr::lgr$appenders$console$set_layout(
    lgr::LayoutFormat$new(timestamp_fmt = "%Y-%m-%d %T"))

  lgr::lgr$info( "CellChatDB: retrieval of ligand-receptor interactions")
  stopifnot(is.character(qgenes))
  stopifnot(!is.null(genedb))
  stopifnot(!is.null(ligand_receptor_db))
  stopifnot(!is.null(ligand_receptor_xref))
  validate_db_df(genedb, dbtype = "genedb")
  validate_db_df(ligand_receptor_db, dbtype = "ligand_receptor_db")
  validate_db_df(ligand_receptor_xref, dbtype = "ligand_receptor_xref")


  query_df <- data.frame("symbol" = qgenes, stringsAsFactors = F)

  all_query_ligand_receptors <- as.data.frame(
    ligand_receptor_xref |>
      dplyr::left_join(
        dplyr::filter(
          dplyr::select(genedb,
                        c("entrezgene",
                          "symbol")),
          !is.na(.data$symbol)),
        by = c("symbol"), relationship = "many-to-many") |>
      dplyr::filter(!is.na(.data$entrezgene)) |>
      dplyr::inner_join(query_df, by = "symbol", relationship = "many-to-many")
  )

  query_hits <- list()
  query_hits[['ligand']] <- all_query_ligand_receptors |>
    dplyr::filter(class == "ligand") |>
    dplyr::select(c("interaction_id"))
  query_hits[['receptor']] <- all_query_ligand_receptors |>
    dplyr::filter(class == "receptor") |>
    dplyr::select(c("interaction_id"))

  valid_query_hits <-
    query_hits[['ligand']] |>
    dplyr::inner_join(query_hits[['receptor']],
                      by = "interaction_id", relationship = "many-to-many")

  ligand_receptor_results <- list()
  ligand_receptor_results[['cell_cell_contact']] <-
    data.frame()
  ligand_receptor_results[['secreted_signaling']] <-
    data.frame()
  ligand_receptor_results[['ecm_receptor']] <-
    data.frame()

  if (NROW(valid_query_hits) > 0) {
    ligand_receptor_results[['cell_cell_contact']] <-
      as.data.frame(
        ligand_receptor_db |>
          dplyr::filter(.data$annotation == "Cell-Cell Contact") |>
          dplyr::inner_join(valid_query_hits,
                            by = "interaction_id", relationship = "many-to-many")
      ) |>
      dplyr::select(-c("interaction_id",
                       "annotation",
                       "interaction_members")) |>
      dplyr::distinct()

    ligand_receptor_results[['secreted_signaling']] <-
      as.data.frame(
        ligand_receptor_db |>
          dplyr::filter(.data$annotation == "Secreted Signaling") |>
          dplyr::inner_join(valid_query_hits,
                            by = "interaction_id", relationship = "many-to-many")
      ) |>
      dplyr::select(-c("interaction_id",
                       "annotation",
                       "interaction_members")) |>
      dplyr::distinct()


    ligand_receptor_results[['ecm_receptor']] <-
      as.data.frame(
        ligand_receptor_db |>
          dplyr::filter(.data$annotation == "ECM-Receptor") |>
          dplyr::inner_join(valid_query_hits,
                            by = "interaction_id", relationship = "many-to-many")
      ) |>
      dplyr::select(-c("interaction_id",
                       "annotation",
                       "interaction_members")) |>
      dplyr::distinct()

  }

  return(ligand_receptor_results)

}