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proximity: Remove use_positions

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This commit is contained in:
Elias Projahn 2021-11-14 17:21:39 +01:00
parent cfc5e7a6bf
commit 7bd63aa6d3
2 changed files with 6 additions and 15 deletions
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9
R/analyze.R
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@ -33,18 +33,15 @@ analyze <- function(preset, progress = NULL) {
# - `score` Score for the gene between 0.0 and 1.0. # - `score` Score for the gene between 0.0 and 1.0.
methods <- list( methods <- list(
"clusteriness" = clusteriness, "clusteriness" = clusteriness,
"correlation" = correlation,
"proximity" = proximity,
"neural" = neural,
"clusteriness_positions" = function(...) { "clusteriness_positions" = function(...) {
clusteriness(..., use_positions = TRUE) clusteriness(..., use_positions = TRUE)
}, },
"correlation" = correlation,
"correlation_positions" = function(...) { "correlation_positions" = function(...) {
correlation(..., use_positions = TRUE) correlation(..., use_positions = TRUE)
}, },
"proximity_positions" = function(...) { "proximity" = proximity,
proximity(..., use_positions = TRUE) "neural" = neural,
},
"neural_positions" = function(...) { "neural_positions" = function(...) {
neural(..., use_positions = TRUE) neural(..., use_positions = TRUE)
} }

12
R/proximity.R
View file

@ -2,24 +2,18 @@
# #
# A score will be given to each gene such that 0.0 corresponds to the maximal # 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. # mean distance across all genes and 1.0 corresponds to a distance of 0.
proximity <- function(preset, use_positions = FALSE, progress = NULL) { proximity <- function(preset, progress = NULL) {
species_ids <- preset$species_ids species_ids <- preset$species_ids
gene_ids <- preset$gene_ids gene_ids <- preset$gene_ids
cached("proximity", c(species_ids, gene_ids, use_positions), { cached("proximity", c(species_ids, gene_ids), {
# Prefilter distances by species and gene. # Prefilter distances by species and gene.
data <- geposan::distances[ data <- geposan::distances[
species %chin% preset$species_ids & gene %chin% preset$gene_ids species %chin% preset$species_ids & gene %chin% preset$gene_ids
] ]
# Compute the score as described above. # Compute the score as described above.
data <- data[, .(mean_distance = mean(distance)), by = "gene"]
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)] max_distance <- data[, max(mean_distance)]
data[, score := 1 - mean_distance / max_distance] data[, score := 1 - mean_distance / max_distance]