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 <[email protected]> --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
scverse · Sep 19, 2023 · bffaf33 · bffaf33
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diff --git 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
@@ -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
diff --git 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()
+```
+