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Use Bioconductor vignette standards #112

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Sep 19, 2023
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Use Bioconductor vignette standards #112

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212e643
Use Bioconductor vignette standards
LouiseDck Sep 19, 2023
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Fix DESCRIPTION
LouiseDck Sep 19, 2023
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LouiseDck Sep 19, 2023
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Merge remote-tracking branch 'origin/main' into vignette
rcannood Sep 19, 2023
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1 change: 1 addition & 0 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ Imports:
R6
Suggests:
anndata,
BiocStyle,
knitr,
reticulate,
rhdf5,
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38 changes: 34 additions & 4 deletions vignettes/getting-started.Rmd
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@@ -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}
---
Expand All @@ -14,10 +21,24 @@
)
```

# 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")

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file=vignettes/getting-started.Rmd,line=36,col=1,[trailing_whitespace_linter] Trailing whitespace is superfluous.
BiocManager::install("BiocStyle")
```

# 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`.


Expand All @@ -30,6 +51,8 @@
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}
Expand All @@ -49,10 +72,11 @@
var <- adata$var
```

## `InMemoryAnnData` backend

The following example details how to construct an InMemoryAnnData and access its contents.

```{r inmemory_construct}

adata <- AnnData(
X = matrix(1:15, 3L, 5L),
layers = list(
Expand Down Expand Up @@ -82,3 +106,9 @@
seurat <- to_Seurat(adata)
```

# Session info

```{r}
sessionInfo()
```

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