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preset: Make reference genes the first parameter

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This commit is contained in:
Elias Projahn 2022-01-17 19:52:51 +01:00
parent 8cda3e8e83
commit c8f1e522f9
2 changed files with 13 additions and 13 deletions
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18
R/preset.R
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@ -9,18 +9,18 @@
#' methods: [clustering()], [correlation()], [neural()], [adjacency()] and
#' [proximity()].
#'
#' @param reference_gene_ids IDs of reference genes to compare to.
#' @param methods List of methods to apply.
#' @param species_ids IDs of species to include.
#' @param gene_ids IDs of genes to screen.
#' @param reference_gene_ids IDs of reference genes to compare to.
#'
#' @return The preset to use with [analyze()].
#'
#' @export
preset <- function(methods = all_methods(),
preset <- function(reference_gene_ids,
methods = all_methods(),
species_ids = geposan::species$id,
gene_ids = geposan::genes$id,
reference_gene_ids) {
gene_ids = geposan::genes$id) {
# Count included species per gene.
genes_n_species <- geposan::distances[
species %chin% species_ids,
@ -39,10 +39,10 @@ preset <- function(methods = all_methods(),
# for the object later.
structure(
list(
reference_gene_ids = sort(reference_gene_ids),
methods = methods,
species_ids = sort(species_ids),
gene_ids = sort(gene_ids_filtered),
reference_gene_ids = sort(reference_gene_ids)
gene_ids = sort(gene_ids_filtered)
),
class = "geposan_preset"
)
@ -60,16 +60,16 @@ print.geposan_preset <- function(x, ...) {
cat(sprintf(
paste0(
"geposan preset:",
"\n Reference genes: %i",
"\n Included methods: %s",
"\n Number of species: %i",
"\n Number of genes: %i",
"\n Reference genes: %i",
"\n"
),
length(x$reference_gene_ids),
paste(sapply(x$methods, function(m) m$id), collapse = ", "),
length(x$species_ids),
length(x$gene_ids),
length(x$reference_gene_ids)
length(x$gene_ids)
))
invisible(x)

8
man/preset.Rd
View file

@ -5,20 +5,20 @@
\title{Create a new preset.}
\usage{
preset(
reference_gene_ids,
methods = all_methods(),
species_ids = geposan::species$id,
gene_ids = geposan::genes$id,
reference_gene_ids
gene_ids = geposan::genes$id
)
}
\arguments{
\item{reference_gene_ids}{IDs of reference genes to compare to.}
\item{methods}{List of methods to apply.}
\item{species_ids}{IDs of species to include.}
\item{gene_ids}{IDs of genes to screen.}
\item{reference_gene_ids}{IDs of reference genes to compare to.}
}
\value{
The preset to use with \code{\link[=analyze]{analyze()}}.