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Reindent code to use just two spaces

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This commit is contained in:
Elias Projahn 2022-05-26 12:42:19 +02:00
parent a1e6147466
commit c04b6337e9
17 changed files with 1583 additions and 1582 deletions
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116
R/preset.R
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@ -21,55 +21,55 @@ preset <- function(reference_gene_ids,
methods = all_methods(),
species_ids = geposan::species$id,
gene_ids = geposan::genes$id) {
# Count included species per gene.
genes_n_species <- geposan::distances[
species %chin% species_ids,
.(n_species = .N),
by = "gene"
]
# Count included species per gene.
genes_n_species <- geposan::distances[
species %chin% species_ids,
.(n_species = .N),
by = "gene"
]
# Filter out genes with less than 25% existing orthologs.
gene_ids_filtered <- genes_n_species[
gene %chin% gene_ids &
n_species >= 0.25 * length(species_ids),
gene
]
# Filter out genes with less than 25% existing orthologs.
gene_ids_filtered <- genes_n_species[
gene %chin% gene_ids &
n_species >= 0.25 * length(species_ids),
gene
]
reference_gene_ids_excluded <- reference_gene_ids[
!reference_gene_ids %chin% gene_ids_filtered
]
reference_gene_ids_excluded <- reference_gene_ids[
!reference_gene_ids %chin% gene_ids_filtered
]
if (length(reference_gene_ids_excluded > 0)) {
warning(paste0(
"The following reference gene IDs are excluded from the preset ",
"because they don't have enough data: ",
paste(reference_gene_ids_excluded, collapse = ", ")
))
}
if (length(reference_gene_ids_excluded > 0)) {
warning(paste0(
"The following reference gene IDs are excluded from the preset ",
"because they don't have enough data: ",
paste(reference_gene_ids_excluded, collapse = ", ")
))
}
reference_gene_ids_included <- reference_gene_ids[
reference_gene_ids %chin% gene_ids_filtered
]
reference_gene_ids_included <- reference_gene_ids[
reference_gene_ids %chin% gene_ids_filtered
]
if (length(reference_gene_ids_included) < 1) {
stop(paste0(
"There has to be at least one reference gene for the preset to be ",
"valid. Please note that some methods may require more reference ",
"genes."
))
}
if (length(reference_gene_ids_included) < 1) {
stop(paste0(
"There has to be at least one reference gene for the preset to be ",
"valid. Please note that some methods may require more reference ",
"genes."
))
}
# The included data gets sorted to be able to produce predictable hashes
# for the object later.
structure(
list(
reference_gene_ids = sort(reference_gene_ids_included),
methods = methods,
species_ids = sort(species_ids),
gene_ids = sort(gene_ids_filtered)
),
class = "geposan_preset"
)
# The included data gets sorted to be able to produce predictable hashes
# for the object later.
structure(
list(
reference_gene_ids = sort(reference_gene_ids_included),
methods = methods,
species_ids = sort(species_ids),
gene_ids = sort(gene_ids_filtered)
),
class = "geposan_preset"
)
}
#' S3 method to print a preset object.
@ -81,20 +81,20 @@ preset <- function(reference_gene_ids,
#'
#' @export
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"
),
length(x$reference_gene_ids),
paste(sapply(x$methods, function(m) m$id), collapse = ", "),
length(x$species_ids),
length(x$gene_ids)
))
cat(sprintf(
paste0(
"geposan preset:",
"\n Reference genes: %i",
"\n Included methods: %s",
"\n Number of species: %i",
"\n Number of genes: %i",
"\n"
),
length(x$reference_gene_ids),
paste(sapply(x$methods, function(m) m$id), collapse = ", "),
length(x$species_ids),
length(x$gene_ids)
))
invisible(x)
invisible(x)
}