geposan/R/method_species_adjacency.R

#' Score genes based on their adjacency to the reference genes within species.
#'
#' For each gene and species, the method will first combine the gene's distances
#' to the reference genes within that species. Afterwards, the results are
#' summarized across species and determine the gene's score.
#'
#' @param distance_estimate Function for combining the distance differences
#'   within one species.
#' @param summarize Function for summarizing the distance values across species.
#'
#' @return An object of class `geposan_method`.
#'
#' @seealso [adjacency()]
#'
#' @export
species_adjacency <- function(distance_estimate = stats::median,
                              summarize = stats::median) {
    method(
        id = "species_adjacency",
        name = "Species adj.",
        description = "Species adjacency",
        function(preset, progress) {
            species_ids <- preset$species_ids
            gene_ids <- preset$gene_ids
            reference_gene_ids <- preset$reference_gene_ids

            cached(
                "species_adjacency",
                c(
                    species_ids,
                    gene_ids,
                    reference_gene_ids,
                    distance_estimate,
                    summarize
                ),
                { # nolint
                    # Prefilter distances.
                    data <- geposan::distances[
                        species %chin% species_ids & gene %chin% gene_ids
                    ]

                    progress_state <- 0.0
                    progress_step <- 0.9 / length(species_ids)

                    # Iterate through all species and find the distance
                    # estimates within that species.
                    for (species_id in species_ids) {
                        # For all genes, compute the distance to one reference
                        # gene at a time in one go.
                        for (reference_gene_id in reference_gene_ids) {
                            comparison_distance <- data[
                                species == species_id &
                                    gene == reference_gene_id,
                                distance
                            ]

                            column <- quote(reference_gene_id)

                            if (length(comparison_distance) != 1) {
                                # If we don't have a comparison distance, we
                                # can't compute a difference. This happens, if
                                # the species doesn't have the reference gene.
                                data[
                                    species == species_id &
                                        gene %chin% gene_ids,
                                    eval(column) := NA_integer_
                                ]
                            } else {
                                data[
                                    species == species_id &
                                        gene %chin% gene_ids,
                                    eval(column) :=
                                        abs(distance - comparison_distance)
                                ]
                            }
                        }

                        # Combine the distances to the different reference genes
                        # into one value using the provided function.
                        data[
                            species == species_id &
                                gene %chin% gene_ids,
                            combined_distance := as.numeric(
                                distance_estimate(na.omit(
                                    # Convert the data.table subset into a
                                    # vector to get the correct na.omit
                                    # behavior.
                                    as.matrix(.SD)[1, ]
                                ))
                            ),
                            .SDcols = reference_gene_ids,
                            by = gene
                        ]

                        progress_state <- progress_state + progress_step
                        progress(progress_state)
                    }

                    progress(0.9)

                    # Remove the distances between the reference genes.
                    for (reference_gene_id in reference_gene_ids) {
                        column <- quote(reference_gene_id)
                        data[gene == reference_gene_id, eval(column) := NA]
                    }

                    # Recompute the combined distance for the reference genes.
                    data[
                        gene %chin% reference_gene_ids,
                        combined_distance := as.numeric(
                            distance_estimate(na.omit(as.matrix(.SD)[1, ]))
                        ),
                        .SDcols = reference_gene_ids,
                        by = list(species, gene)
                    ]

                    # Combine the distances into one value.
                    results <- data[,
                        .(
                            summarized_distances = as.numeric(
                                summarize(na.omit(combined_distance))
                            )
                        ),
                        by = gene
                    ]

                    # Compute the final score by normalizing the difference.
                    results[
                        ,
                        score := 1 - summarized_distances /
                            max(summarized_distances)
                    ]

                    progress(1.0)

                    result(
                        method = "species_adjacency",
                        scores = results[, .(gene, score)],
                        details = list(
                            data = data,
                            results = results
                        )
                    )
                }
            )
        }
    )
}