diff --git a/DESCRIPTION b/DESCRIPTION
index 1f1dfd9..4e9888d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,9 +5,10 @@ Authors@R:
     person("Kari", "Lavikka", , "kari.lavikka@helsinki.fi", 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
\ No newline at end of file
+    Software
diff --git a/R/clonevol_functions.R b/R/clonevol_functions.R
index 0786209..da6cea3 100644
--- a/R/clonevol_functions.R
+++ b/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")
   }
diff --git a/R/jellyfisher.R b/R/jellyfisher.R
index a42103b..41050bb 100644
--- a/R/jellyfisher.R
+++ b/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,
     )
   )
 }
-
diff --git a/R/utils.R b/R/utils.R
index 7a6b4ae..a76e3fb 100644
--- a/R/utils.R
+++ b/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),
diff --git a/man/extract_tables_from_clonevol.Rd b/man/extract_tables_from_clonevol.Rd
index 24445f9..a5ab43e 100644
--- a/man/extract_tables_from_clonevol.Rd
+++ b/man/extract_tables_from_clonevol.Rd
@@ -4,12 +4,12 @@
 \alias{extract_tables_from_clonevol}
 \title{Extract samples, phylogeny, and subclonal compositions from ClonEvol results}
 \usage{
-extract_tables_from_clonevol(y, model = 1, explicit_parents = list())
+extract_tables_from_clonevol(y, model = 1)
 }
 \arguments{
 \item{y}{A ClonEvol object}
 
-\item{model}{The model to extract from}
+\item{model}{The model to extract. Defaults to 1}
 }
 \value{
 A named list with three data frames: samples, phylogeny, and compositions
@@ -17,3 +17,14 @@ A named list with three data frames: samples, phylogeny, and compositions
 \description{
 Extracts data frames that can be used to create a Jellyfish plot.
 }
+\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()
+}
+
+}
diff --git a/man/jellyfisher.Rd b/man/jellyfisher.Rd
index 9631722..6579147 100644
--- a/man/jellyfisher.Rd
+++ b/man/jellyfisher.Rd
@@ -82,11 +82,13 @@ https://github.com/HautaniemiLab/jellyfish?tab=readme-ov-file#input-data
 }
 \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
+  )
+)
 
 }
diff --git a/man/select_patients.Rd b/man/select_patients.Rd
index 99469ff..fbccd5b 100644
--- a/man/select_patients.Rd
+++ b/man/select_patients.Rd
@@ -17,3 +17,9 @@ A list of tables filtered by patient
 \description{
 Given a list of tables, filter them by patient.
 }
+\examples{
+data(jellyfisher_example_tables)
+jellyfisher_example_tables |>
+  select_patients("EOC809")
+
+}
diff --git a/man/validate_tables.Rd b/man/validate_tables.Rd
index 9293663..0ad315b 100644
--- a/man/validate_tables.Rd
+++ b/man/validate_tables.Rd
@@ -12,3 +12,8 @@ validate_tables(tables)
 \description{
 Superficially validate that the tables are in the correct format.
 }
+\examples{
+data(jellyfisher_example_tables)
+validate_tables(jellyfisher_example_tables)
+
+}
diff --git a/tools/generate-R-code.mjs b/tools/generate-R-code.mjs
index 7d8419e..43d9d2a 100755
--- a/tools/generate-R-code.mjs
+++ b/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,