From bffaf33d39bb7ae1b9b1098a62fdd8af13349931 Mon Sep 17 00:00:00 2001
From: Louise Deconinck <36621934+LouiseDck@users.noreply.github.com>
Date: Tue, 19 Sep 2023 12:46:56 +0200
Subject: [PATCH] Use Bioconductor vignette standards (#112)

* Use Bioconductor vignette standards

* Fix DESCRIPTION

* Linting indentation typo

* Run styler and fix lintr issues

* Apply suggestions from code review

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 DESCRIPTION                   |  1 +
 R/write_h5ad.R                |  2 +-
 man/write_h5ad.Rd             |  2 +-
 vignettes/getting-started.Rmd | 37 ++++++++++++++++++++++++++++++++---
 4 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cec7d974..c9b5b0a8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -54,6 +54,7 @@ Imports:
     R6
 Suggests:
     anndata,
+    BiocStyle,
     knitr,
     reticulate,
     rhdf5,
diff --git a/R/write_h5ad.R b/R/write_h5ad.R
index c1fb0411..df3e2c98 100644
--- a/R/write_h5ad.R
+++ b/R/write_h5ad.R
@@ -30,7 +30,7 @@
 #'   ncells <- 100
 #'   counts <- matrix(rpois(20000, 5), ncol = ncells)
 #'   logcounts <- log2(counts + 1)
-#'   #
+#'
 #'   pca <- matrix(runif(ncells * 5), ncells)
 #'   tsne <- matrix(rnorm(ncells * 2), ncells)
 #'
diff --git a/man/write_h5ad.Rd b/man/write_h5ad.Rd
index f47d835c..9247ca6b 100644
--- a/man/write_h5ad.Rd
+++ b/man/write_h5ad.Rd
@@ -39,7 +39,7 @@ if (requireNamespace("SingleCellExperiment", quietly = TRUE)) {
   ncells <- 100
   counts <- matrix(rpois(20000, 5), ncol = ncells)
   logcounts <- log2(counts + 1)
-  #
+
   pca <- matrix(runif(ncells * 5), ncells)
   tsne <- matrix(rnorm(ncells * 2), ncells)
 
diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd
index f35a3289..360b4497 100644
--- a/vignettes/getting-started.Rmd
+++ b/vignettes/getting-started.Rmd
@@ -1,8 +1,15 @@
 ---
-title: "Getting Started"
-output: rmarkdown::html_vignette
+title: "Using anndataR to read and convert"
+shorttitle: "Using anndataR"
+author:
+  - name: Robrecht Cannoodt
+  - name: Luke Zappia
+  - name: Martin Morgan
+  - name: Louise Deconinck
+package: anndataR
+output: BiocStyle::html_document
 vignette: >
-  %\VignetteIndexEntry{Getting Started}
+  %\VignetteIndexEntry{Using anndataR to read and convert}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -14,10 +21,24 @@ knitr::opts_chunk$set(
 )
 ```
 
+# Introduction
+
 This package allows users to work with `.h5ad` files, access various slots in the datasets and convert these files to `SingleCellExperiment` objects and `SeuratObject`s, and vice versa.
 
 Check out `?anndataR` for a full list of the functions provided by this package.
 
+# Installation
+
+Install using:
+```{r, eval = FALSE}
+if (!require("BiocManager", quietly = TRUE)) {
+  install.packages("BiocManager")
+}
+BiocManager::install("anndataR")
+```
+
+# Usage
+
 This package provides an abstract interface for `AnnData` objects. This abstract interface models its Python counterpart closely, and stores a data matrix `X` and annotations corresponding to observations (`obs`, `obsm`, `obsp`) and variables (`var`, `varm`, `varp`) and unstructured metadata `uns`.
 
 
@@ -30,6 +51,8 @@ This abstract interface is implemented by different backends. Currently, the fol
 The `InMemoryAnnData` backend allows you to construct an `AnnData` object in memory.
 The `HDF5AnnData` backend allows you to read in an `AnnData` object from an `.h5ad` file.
 
+## `HDF5AnnData` backend
+
 Here is an example of how to read in an `.h5ad` file.
 
 ```{r setup}
@@ -49,6 +72,8 @@ obs <- adata$obs
 var <- adata$var
 ```
 
+## `InMemoryAnnData` backend
+
 The following example details how to construct an InMemoryAnnData and access its contents.
 
 ```{r inmemory_construct}
@@ -81,3 +106,9 @@ sce <- to_SingleCellExperiment(adata)
 seurat <- to_Seurat(adata)
 ```
 
+# Session info
+
+```{r}
+sessionInfo()
+```
+