improve docs

DESCRIPTION

@@ -5,9 +5,10 @@ Authors@R:
     person("Kari", "Lavikka", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4163-4945"))
 Description:
-    'Jellyfisher' creates Jellyfish plots using the JavaScript based
-    'Jellyfish' library. Jellyfish plots integrate both phylogenetic
-    and sample tree structures in a single visualization.
+    Jellyfisher creates interactive Jellyfish plots for tumor evolution
+    visualization. These plots integrate a hierarchical sample structure
+    and tumor phylogeny into a single visualization, allowing for the
+    display of both spatial and temporal dimensions of the tumor evolution. 
 License: MIT
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -27,4 +28,4 @@ VignetteBuilder: knitr
 biocViews:
     Visualization,
     Phylogenetics,
-    Software
+    Software

R/clonevol_functions.R

@@ -3,16 +3,26 @@
 #' Extracts data frames that can be used to create a Jellyfish plot.
 #'
 #' @param y A ClonEvol object
-#' @param model The model to extract from
+#' @param model The model to extract. Defaults to 1
 #'
 #' @return A named list with three data frames: samples, phylogeny, and compositions
 #'
 #' @import dplyr
 #' @import stringr
 #'
+#' @examples
+#' if (requireNamespace("clonevol", quietly = TRUE)) {
+#'   # Run ClonEvol. Check the ClonEvol documentation for details.
+#'   y <- infer.clonal.models(...)
+#'
+#'   # Plot the results
+#'   extract_tables_from_clonevol(y, model = 1) |>
+#'     jellyfisher()
+#' }
+#'
 #' @export
 #'
-extract_tables_from_clonevol <- function(y, model = 1, explicit_parents = list()) {
+extract_tables_from_clonevol <- function(y, model = 1) {
   if (!requireNamespace("clonevol", quietly = TRUE)) {
     stop("The clonevol package must be installed to use this functionality")
   }

R/jellyfisher.R

@@ -1,4 +1,3 @@
-
 # Auto-generated by generate-R-code.mjs
 # Do not edit this file manually
 
@@ -64,12 +63,14 @@
 #'
 #' @examples
 #' # Plot the bundled example data
+#' data(jellyfisher_example_tables)
 #' jellyfisher(jellyfish_example_tables,
-#'             options = list(
-#'               sampleHeight = 70,
-#'               sampleTakenGuide = "none",
-#'               showLegend = FALSE
-#'             ))
+#'   options = list(
+#'     sampleHeight = 70,
+#'     sampleTakenGuide = "none",
+#'     showLegend = FALSE
+#'   )
+#' )
 #'
 #' @import htmlwidgets
 #' @export
@@ -194,7 +195,7 @@ jellyfisher <- function(tables,
   x <- list(
     tables = tables,
     options = options,
-    controls = controls 
+    controls = controls
   )
 
   # Create widget
@@ -213,4 +214,3 @@ jellyfisher <- function(tables,
     )
   )
 }
-

R/utils.R

@@ -7,6 +7,11 @@
 #'
 #' @return A list of tables filtered by patient
 #'
+#' @examples
+#' data(jellyfisher_example_tables)
+#' jellyfisher_example_tables |>
+#'   select_patients("EOC809")
+#'
 #' @export
 #'
 select_patients <- function(tables, patient) {
@@ -24,6 +29,10 @@ select_patients <- function(tables, patient) {
 #'
 #' @param tables A list of tables (samples, phylogeny, compositions)
 #'
+#' @examples
+#' data(jellyfisher_example_tables)
+#' validate_tables(jellyfisher_example_tables)
+#'
 validate_tables <- function(tables) {
   stopifnot(
     is.data.frame(tables$samples),

tools/generate-R-code.mjs

@@ -145,6 +145,7 @@ ${roxygenOptions.join("\n")}
 #'
 #' @examples
 #' # Plot the bundled example data
+#' data(jellyfisher_example_tables)
 #' jellyfisher(jellyfish_example_tables,
 #'             options = list(
 #'               sampleHeight = 70,