method: Add context help

R/method.R

@@ -3,6 +3,7 @@
 #' @param id Unique identifier for the method.
 #' @param name Human readable name.
 #' @param description Slightly longer description.
+#' @param help Context help for user interfaces.
 #' @param func Function to apply the method. The function should accept two
 #'   parameters: an object of class `geposan_preset` as input and a function to
 #'   report progress information to as a numeric value. The return value should
@@ -11,10 +12,11 @@
 #' @return An object of class `geposan_method`.
 #'
 #' @export
-method <- function(id, name, description, func) {
+method <- function(id, name, description, help, func) {
   stopifnot(is.character(id) & length(id) == 1)
   stopifnot(is.character(name) & length(name) == 1)
   stopifnot(is.character(description) & length(description) == 1)
+  stopifnot(is.character(help) & length(help) == 1)
   stopifnot(is.function(func))
 
   structure(
@@ -22,6 +24,7 @@ method <- function(id, name, description, func) {
       id = glue::glue("geposan_method_{id}"),
       name = name,
       description = description,
+      help = help,
       func = func
     ),
     class = "geposan_method"

R/method_adjacency.R

@@ -22,6 +22,11 @@ adjacency <- function(id = "adjacency",
     id = id,
     name = name,
     description = description,
+    help = paste0(
+      "Adjacency to the reference genes across species. This method penalizes ",
+      "genes that do not occur in the region typical for the reference genes, ",
+      "without artificially defining a fixed boundary."
+    ),
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_clustering.R

@@ -73,6 +73,10 @@ clustering <- function(id = "clustering",
     id = id,
     name = name,
     description = description,
+    help = paste0(
+      "Proportion of orthologs that have similar telomeric distances across ",
+      "species. This favors genes whose position is evolutionarily conserved."
+    ),
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_correlation.R

@@ -18,6 +18,12 @@ correlation <- function(id = "correlation",
     id = id,
     name = name,
     description = description,
+    help = paste0(
+      "Spearman's rank correlation of the telomeric distances of the gene in ",
+      "comparison with the reference gene set. This helps to assess if the ",
+      "gene is as close or distant to telomeres as the reference genes within ",
+      "each species."
+    ),
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_distance.R

@@ -21,6 +21,7 @@ distance <- function(id = "distance",
     id = id,
     name = name,
     description = description,
+    help = "Median distance to the telomeres across species.",
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

R/method_random_forest.R

@@ -28,6 +28,11 @@ random_forest <- function(id = "rforest",
     id = id,
     name = name,
     description = description,
+    help = paste0(
+      "Assessment of a random forest model trained on reference gene ",
+      "distances. It may derive patterns in positional data that have not ",
+      "been covered by other methods."
+    ),
     function(preset, progress) {
       species_ids <- preset$species_ids
       gene_ids <- preset$gene_ids

man/method.Rd

@@ -4,7 +4,7 @@
 \alias{method}
 \title{Describe a new method for analyzing gene position data.}
 \usage{
-method(id, name, description, func)
+method(id, name, description, help, func)
 }
 \arguments{
 \item{id}{Unique identifier for the method.}
@@ -13,6 +13,8 @@ method(id, name, description, func)
 
 \item{description}{Slightly longer description.}
 
+\item{help}{Context help for user interfaces.}
+
 \item{func}{Function to apply the method. The function should accept two
 parameters: an object of class \code{geposan_preset} as input and a function to
 report progress information to as a numeric value. The return value should