chore: use lazy example data

I've been switching between lazy and non-lazy. Bioconductor expects non-lazy, but as we are submitting to CRAN, after all, lazy data should be used.
HautaniemiLab · Feb 2, 2025 · 4442a6b · 4442a6b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,7 +12,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-LazyData: false
+LazyData: true
 URL: https://github.com/HautaniemiLab/jellyfisher, https://hautaniemilab.github.io/jellyfisher/
 BugReports: https://github.com/HautaniemiLab/jellyfisher/issues
 Imports:

diff --git a/R/jellyfisher.R b/R/jellyfisher.R
@@ -80,7 +80,6 @@
 #'
 #' @examples
 #' # Plot the bundled example data
-#' data(jellyfisher_example_tables)
 #' jellyfisher(jellyfisher_example_tables,
 #'             options = list(
 #'               sampleHeight = 70,

diff --git a/R/utils.R b/R/utils.R
@@ -8,7 +8,6 @@
 #' @return A list of tables filtered by patient
 #'
 #' @examples
-#' data(jellyfisher_example_tables)
 #' jellyfisher_example_tables |>
 #'   select_patients("EOC809")
 #'
@@ -96,7 +95,6 @@ validate_tables <- function(tables) {
 #' @return A list of tables with parents set for each sample
 #'
 #' @examples
-#' data(jellyfisher_example_tables)
 #' jellyfisher_example_tables |>
 #'   select_patients("EOC809") |>
 #'   set_parents(list("EOC809_r1Bow1_DNA1" = "EOC809_p2Per1_cO_DNA2")) |>
@@ -145,7 +143,6 @@ set_parents <- function(tables, parents, unset_missing = FALSE) {
 #' @return A list of tables with ranks set for each sample
 #'
 #' @examples
-#' data(jellyfisher_example_tables)
 #' jellyfisher_example_tables |>
 #'   select_patients("EOC809") |>
 #'   set_ranks(list("EOC809_r1Bow1_DNA1" = 2, "EOC809_p2Per1_cO_DNA2" = 2),

diff --git a/README.md b/README.md
@@ -45,7 +45,6 @@ function's documentation.
 library(jellyfisher)
 
 # Plot the bundled example data
-data("jellyfisher_example_tables")
 jellyfisher(jellyfisher_example_tables)
 ```
 

diff --git a/man/jellyfisher.Rd b/man/jellyfisher.Rd
diff --git a/man/select_patients.Rd b/man/select_patients.Rd
diff --git a/man/set_parents.Rd b/man/set_parents.Rd
diff --git a/man/set_ranks.Rd b/man/set_ranks.Rd
diff --git a/tools/generate-R-code.mjs b/tools/generate-R-code.mjs
@@ -150,7 +150,6 @@ ${roxygenOptions.join("\n")}
 #'
 #' @examples
 #' # Plot the bundled example data
-#' data(jellyfisher_example_tables)
 #' jellyfisher(jellyfisher_example_tables,
 #'             options = list(
 #'               sampleHeight = 70,

diff --git a/vignettes/introduction.Rmd b/vignettes/introduction.Rmd
@@ -31,17 +31,13 @@ making it compatible with various tools and workflows.
 The input data should follow specific structures for _samples_, _phylogeny_, 
 subclonal _compositions_, and optional _ranks_.
 
-The Jellyfisher package includes an example data set based on the following
-publication:
+The `jellyfisher` package includes an example data set
+(`jellyfisher_example_tables`) based on the following publication:  
 Lahtinen, A., Lavikka, K., Virtanen, A., et al. "Evolutionary states and
 trajectories characterized by distinct pathways stratify patients with ovarian
 high-grade serous carcinoma." _Cancer Cell_ **41**, 1103–1117.e12 (2023). DOI:
 [10.1016/j.ccell.2023.04.017](https://doi.org/10.1016/j.ccell.2023.04.017).
 
-```{r}
-data(jellyfisher_example_tables)
-```
-
 ```{r echo=F, message=F}
 # Subset the data to keep the compiled vignette a bit smaller
 jellyfisher_example_tables <- jellyfisher_example_tables |>