fix vignette

cran-comments.md

@@ -1,14 +1,17 @@
+Resubmission: moved some examples to `\donttest{}` to reduce checking time.
+
 # dyngen 1.0.0
 
 This version mostly upgrades dyngen's ease-of-use, such as better vignettes, conversion functions for working with dyngen datasets in other packages, and more useful ways of specifying platform-specific parameters (i.e. number of cores and cache location). Perhaps more excitingly, the dyngen documentation is more readable online at [https://dyngen.dynverse.org](https://dyngen.dynverse.org)!
 
-## NEW FEATURES
+## BREAKING CHANGES
+* `wrap_dataset()`: Now returns a list instead of a dyno object. Use `as_dyno(model)` or `wrap_dataset(model, format = "dyno")` to replicate previous behaviour.
 
-* `as_anndata()`: Added a function for converting the dyngen output to an anndata object.
+## NEW FEATURES
 
-* `as_sce()`: Added a function for converting the dyngen output to an SingleCellExperiment object.
+* Added functions for converting the dyngen output to various data formats: `as_anndata()` for anndata, `as_sce()` for SingleCellExperiment, `as_seurat()` for Seurat, `as_dyno()` for dyno, `as_list()` for a simple list object.
 
-* `as_seurat()`: Added a function for converting the dyngen output to a Seurat object.
+* `wrap_dataset()`: Added 'format' argument which allows choosing the output format (#28).
 
 * The default number of cores used can be set by adding `options(Ncpus = ...)` to your Rprofile.
 
@@ -20,15 +23,14 @@ This version mostly upgrades dyngen's ease-of-use, such as better vignettes, con
 
 ## MAJOR CHANGES
 
-* `generate_experiment()`: Map count density of reference dataset to simulation expression before sampling molecules.
+* `generate_experiment()`: Map count density of reference dataset to simulation expression before sampling molecules. 
+  Parameters are available for toggling off or on the mapping of the reference library size & CPM distribution.
 
 ## MINOR CHANGES
 
 * `initialise_model()`: Change defaults of `num_cores` and `download_cache_dir`
   to `getOption("Ncpus")` and `getOption("dyngen_download_cache_dir")` respectively.
 
-* `as_dyno()`: Rename `wrap_dataset()` to `as_dyno()`.
-
 * `generate_experiment()`: Drastically speed up sampling of molecules.
 
 ## BUG FIX
@@ -39,14 +41,17 @@ This version mostly upgrades dyngen's ease-of-use, such as better vignettes, con
 
 ## DOCUMENTATION
 
-* Extended vignettes:
+* Added and extended vignettes:
   - Advanced: Simulating batch effects
   - Advanced: Simulating a knockout experiment
   - Advanced: Running dyngen from a docker container
   - Advanced: Constructing a custom backbone
   - Advanced: Tweaking parameters
   - Advanced: Comparison of characteristic features between dyngen and reference datasets
 
+* Created a website at [https://dyngen.dynverse.org](https://dyngen.dynverse.org) using pkgdown.
+
+* Shortened examples to reduce r cmd check time.
 
 ## Test environments
 * local Fedora 32 install (R 4.0)

vignettes/getting_started.Rmd

@@ -173,7 +173,7 @@ write_rds(dataset, "dataset.rds", compress = "gz")
 ```
 
 ## Step 8 alternative: Convert to an anndata/SCE/Seurat object
-dyngen (>= 0.4.1) allows converting the output to an `anndata`, `SCE` or `Seurat` object as well.
+dyngen 1.0.0 allows converting the output to an `anndata`, `SCE` or `Seurat` object as well.
 Check out the [anndata documentation](https://cran.r-project.org/package=anndata) 
 on how to install anndata for R.
 
@@ -182,9 +182,13 @@ library(anndata)
 ad <- as_anndata(model)
 ad$write_h5ad("dataset.h5ad")
 
+library(SingleCellExperiment)
 sce <- as_sce(model)
+write_rds(sce, "dataset_sce.rds")
 
-seurat <- as_seurat(model) 
+library(Seurat)
+seurat <- as_seurat(model)
+write_rds(seurat, "dataset_seurat.rds")
 ```
 
 # One-shot function
@@ -194,6 +198,7 @@ all of the steps all at once and producing plots.
 ```{r oneshot_run, message=FALSE, fig.width=20, fig.height=20}
 out <- generate_dataset(
   config,
+  format = "dyno",
   make_plots = TRUE
 )
 

vignettes/getting_started.md

@@ -253,8 +253,8 @@ write_rds(dataset, "dataset.rds", compress = "gz")
 
 ## Step 8 alternative: Convert to an anndata/SCE/Seurat object
 
-dyngen (>= 0.4.1) allows converting the output to an `anndata`, `SCE`
-or `Seurat` object as well. Check out the [anndata
+dyngen 1.0.0 allows converting the output to an `anndata`, `SCE` or
+`Seurat` object as well. Check out the [anndata
 documentation](https://cran.r-project.org/package=anndata) on how to
 install anndata for R.
 
@@ -263,9 +263,13 @@ library(anndata)
 ad <- as_anndata(model)
 ad$write_h5ad("dataset.h5ad")
 
+library(SingleCellExperiment)
 sce <- as_sce(model)
+write_rds(sce, "dataset_sce.rds")
 
-seurat <- as_seurat(model) 
+library(Seurat)
+seurat <- as_seurat(model)
+write_rds(seurat, "dataset_seurat.rds")
 ```
 
 # One-shot function
@@ -276,6 +280,7 @@ all at once and producing plots.
 ``` r
 out <- generate_dataset(
   config,
+  format = "dyno",
   make_plots = TRUE
 )
 ```
@@ -292,7 +297,17 @@ print(out$plot)
 
 ``` r
 library(dyno)
+```
+
+    ## Loading required package: dynfeature
+
+    ## Loading required package: dynguidelines
 
+    ## Loading required package: dynmethods
+
+    ## Loading required package: dynwrap
+
+``` r
 plot_dimred(dataset)
 ```