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Implement all methods using positions additionally

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Elias Projahn 2021-11-05 19:49:54 +01:00
parent 9cbc127177
commit cfc5e7a6bf
5 changed files with 222 additions and 167 deletions
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19
R/proximity.R
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@ -2,21 +2,26 @@
#
# A score will be given to each gene such that 0.0 corresponds to the maximal
# mean distance across all genes and 1.0 corresponds to a distance of 0.
proximity <- function(preset, progress = NULL) {
proximity <- function(preset, use_positions = FALSE, progress = NULL) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
cached("proximity", c(species_ids, gene_ids), {
cached("proximity", c(species_ids, gene_ids, use_positions), {
# Prefilter distances by species and gene.
distances <- geposan::distances[
data <- geposan::distances[
species %chin% preset$species_ids & gene %chin% preset$gene_ids
]
# Compute the score as described above.
distances <- distances[, .(mean_distance = mean(distance)), by = "gene"]
max_distance <- distances[, max(mean_distance)]
distances[, score := 1 - mean_distance / max_distance]
data <- if (use_positions) {
data[, .(mean_distance = mean(position)), by = "gene"]
} else {
data[, .(mean_distance = mean(distance)), by = "gene"]
}
max_distance <- data[, max(mean_distance)]
data[, score := 1 - mean_distance / max_distance]
if (!is.null(progress)) {
# We do everything in one go, so it's not possible to report
@ -25,6 +30,6 @@ proximity <- function(preset, progress = NULL) {
progress(1.0)
}
distances[, .(gene, score)]
data[, .(gene, score)]
})
}