Fix some package issues

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^scripts$
+^cache$

R/comparison.R

@@ -24,7 +24,7 @@ compare <- function(ranking, comparison_gene_ids) {
 
     comparison_ranking <- ranking[gene %chin% comparison_gene_ids]
 
-    p_value <- wilcox.test(
+    p_value <- stats::wilcox.test(
         x = comparison_ranking[, score],
         y = ranking[!gene %chin% comparison_gene_ids, score],
         alternative = "greater"
@@ -46,10 +46,13 @@ compare <- function(ranking, comparison_gene_ids) {
 
 #' S3 method to print a comparison object.
 #'
+#' @param x The comparison to print.
+#' @param ... Other parameters.
+#'
 #' @seealso [compare()]
 #'
 #' @export
-print.geposan_comparison <- function(comparison, ...) {
+print.geposan_comparison <- function(x, ...) {
     cat("geposan comparison:")
     cat(sprintf(
         paste(
@@ -62,14 +65,14 @@ print.geposan_comparison <- function(comparison, ...) {
             "\n\n  p-value for better ranking: %.4f\n",
             sep = ""
         ),
-        comparison$mean,
-        comparison$min,
-        comparison$max,
-        comparison$mean_rank,
-        comparison$first_rank,
-        comparison$last_rank,
-        comparison$p_value
+        x$mean,
+        x$min,
+        x$max,
+        x$mean_rank,
+        x$first_rank,
+        x$last_rank,
+        x$p_value
     ))
 
-    invisible(comparison)
+    invisible(x)
 }

R/plots.R

@@ -41,7 +41,12 @@ plot_scores <- function(ranking, gene_sets = NULL, labels = NULL) {
         }
 
         # Include gene information which will be used for labeling
-        gene_set_data <- merge(gene_set_data, genes, by.x = "gene", by.y = "id")
+        gene_set_data <- merge(
+            gene_set_data,
+            geposan::genes,
+            by.x = "gene",
+            by.y = "id"
+        )
 
         plot <- plot |> plotly::add_trace(
             data = gene_set_data,

R/preset.R

@@ -43,24 +43,27 @@ preset <- function(methods = c(
 
 #' S3 method to print a preset object.
 #'
+#' @param x The preset to print.
+#' @param ... Other parameters.
+#'
 #' @seealso [preset()]
 #'
 #' @export
-print.geposan_preset <- function(preset, ...) {
+print.geposan_preset <- function(x, ...) {
     cat("geposan preset:")
     cat("\n  Included methods: ")
-    cat(preset$method_ids, sep = ", ")
+    cat(x$method_ids, sep = ", ")
 
     cat(sprintf(
         "\n  Input data: %i species, %i genes",
-        length(preset$species_ids),
-        length(preset$gene_ids)
+        length(x$species_ids),
+        length(x$gene_ids)
     ))
 
     cat(sprintf(
         "\n  Comparison data: %i reference genes\n",
-        length(preset$reference_gene_ids)
+        length(x$reference_gene_ids)
     ))
 
-    invisible(preset)
+    invisible(x)
 }

man/print.geposan_comparison.Rd

@@ -4,7 +4,12 @@
 \alias{print.geposan_comparison}
 \title{S3 method to print a comparison object.}
 \usage{
-\method{print}{geposan_comparison}(comparison, ...)
+\method{print}{geposan_comparison}(x, ...)
+}
+\arguments{
+\item{x}{The comparison to print.}
+
+\item{...}{Other parameters.}
 }
 \description{
 S3 method to print a comparison object.

man/print.geposan_preset.Rd

@@ -4,7 +4,12 @@
 \alias{print.geposan_preset}
 \title{S3 method to print a preset object.}
 \usage{
-\method{print}{geposan_preset}(preset, ...)
+\method{print}{geposan_preset}(x, ...)
+}
+\arguments{
+\item{x}{The preset to print.}
+
+\item{...}{Other parameters.}
 }
 \description{
 S3 method to print a preset object.