geposan/R/correlation.R

#' Compute the mean correlation coefficient comparing gene distances with a set
#' of reference genes.
#'
#' @return An object of class `geposan_method`.
#'
#' @export
correlation <- function() {
    method(
        id = "correlation",
        name = "Correlation",
        description = "Correlation with reference genes",
        function(preset, progress) {
            species_ids <- preset$species_ids
            gene_ids <- preset$gene_ids
            reference_gene_ids <- preset$reference_gene_ids

            cached(
                "correlation",
                c(species_ids, gene_ids, reference_gene_ids),
                { # nolint
                    # Prefilter distances by species.
                    distances <- geposan::distances[species %chin% species_ids]

                    # Tranform data to get species as rows and genes as columns.
                    # We construct columns per species, because it requires
                    # fewer iterations, and transpose the table afterwards.

                    data <- data.table(gene = gene_ids)

                    # Make a column containing distance data for each species.
                    for (species_id in species_ids) {
                        species_data <- distances[
                            species == species_id,
                            .(gene, distance)
                        ]

                        data <- merge(data, species_data, all.x = TRUE)
                        setnames(data, "distance", species_id)
                    }

                    # Transpose to the desired format.
                    data <- transpose(data, make.names = "gene")

                    progress(0.33)

                    # Take the reference data.
                    reference_data <- data[, ..reference_gene_ids]

                    # Perform the correlation between all possible pairs.
                    results <- stats::cor(
                        data[, ..gene_ids],
                        reference_data,
                        use = "pairwise.complete.obs",
                        method = "spearman"
                    )

                    results <- data.table(results, keep.rownames = TRUE)
                    setnames(results, "rn", "gene")

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

                    progress(0.66)

                    # Compute the final score as the mean of known correlation
                    # scores. Negative correlations will correctly lessen the
                    # score, which will be clamped to zero as its lower bound.
                    # Genes with no possible correlations at all will be assumed
                    # to have a score of 0.0.

                    compute_score <- function(scores) {
                        score <- mean(scores, na.rm = TRUE)

                        if (is.na(score) | score < 0.0) {
                            score <- 0.0
                        }

                        score
                    }

                    results[,
                        score := compute_score(as.matrix(.SD)),
                        .SDcols = reference_gene_ids,
                        by = gene
                    ]

                    results[, .(gene, score)]

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