add vignette

.gitignore

@@ -5,3 +5,4 @@
 .DS_Store
 .quarto
 *.Rproj
+inst/doc

DESCRIPTION

@@ -17,3 +17,12 @@ Depends:
     ExperimentHub
 Imports: 
     utils
+Suggests: 
+    BiocStyle,
+    SingleCellExperiment,
+    knitr,
+    RefManageR,
+    rmarkdown,
+    sessioninfo,
+    testthat
+VignetteBuilder: knitr

NAMESPACE

@@ -1,4 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
+export(human_gene_transcript_sce)
 importFrom(ExperimentHub,createHubAccessors)
 importFrom(utils,read.csv)

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/human_gene_transcript_sce.Rmd

@@ -0,0 +1,176 @@
+---
+title: "Human retinal organoid data"
+author: 
+  - name: Your name
+    affiliation:
+    - Your institution
+    email: [email protected]
+output: 
+  BiocStyle::html_document:
+    self_contained: yes
+    toc: true
+    toc_float: true
+    toc_depth: 2
+    code_folding: show
+date: "`r doc_date()`"
+package: "`r pkg_ver('chevreuldata')`"
+vignette: >
+  %\VignetteIndexEntry{human_gene_transcript_sce}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}  
+---
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+    collapse = TRUE,
+    comment = "#>",
+    crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html
+)
+```
+
+
+```{r vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE}
+## Track time spent on making the vignette
+startTime <- Sys.time()
+
+## Bib setup
+library("RefManageR")
+library(SingleCellExperiment)
+
+## Write bibliography information
+bib <- c(
+    R = citation(),
+    BiocStyle = citation("BiocStyle")[1],
+    knitr = citation("knitr")[1],
+    RefManageR = citation("RefManageR")[1],
+    rmarkdown = citation("rmarkdown")[1],
+    sessioninfo = citation("sessioninfo")[1],
+    testthat = citation("testthat")[1],
+    chevreuldata = citation("chevreuldata")[1]
+)
+```
+
+# Basics
+
+## Install `chevreuldata`
+
+`R` is an open-source statistical environment which can be easily modified to enhance its functionality via packages. `r Biocpkg("chevreuldata")` is a `R` package available via the [Bioconductor](http://bioconductor.org) repository for packages. `R` can be installed on any operating system from [CRAN](https://cran.r-project.org/) after which you can install `r Biocpkg("chevreuldata")` by using the following commands in your `R` session:
+
+```{r "install", eval = FALSE}
+if (!requireNamespace("BiocManager", quietly = TRUE)) {
+      install.packages("BiocManager")
+  }
+
+BiocManager::install("chevreuldata")
+
+## Check that you have a valid Bioconductor installation
+BiocManager::valid()
+```
+
+## Required knowledge
+
+`r Biocpkg("chevreuldata")` is an `r Biocpkg("ExperimentHub")` based data package containing smart-seq based scRNA-seq data as a `r Biocpkg("SingleCellExperiment")` object from human retinal organoids. All included data is generated by the Cobrinik laboratory at Children's Hospital Los Angeles. 
+
+## Citing `chevreuldata`
+
+We hope that `r Biocpkg("chevreuldata")` will be useful for your research. Please use the following information to cite the package and the overall approach. Thank you!
+
+```{r "citation"}
+## Citation info
+citation("chevreuldata")
+```
+
+# Quick start to using `chevreuldata`
+
+```{r "start", message=FALSE}
+library("chevreuldata")
+```
+
+To access data use helper functions as below
+
+```{r}
+chevreul_sce <- chevreuldata::human_gene_transcript_sce()
+```
+
+Data has been processed using the `r Biocpkg("chevreul")` package. Expression information is available for both gene (main experiment) and transcript (alt experiment) features
+
+```{r}
+mainExpName(chevreul_sce)
+```
+
+```{r}
+altExpNames(chevreul_sce)
+```
+
+cell metadata includes organoid age `Age`, preparation method `Prep.Method`, and louvain clustering identities at multiple resolutions `gene_snn_res.x.x` 
+
+```{r}
+colData(chevreul_sce)
+```
+
+For more information on data generation consult Shayler et al. https://www.biorxiv.org/content/10.1101/2023.02.28.530247v1
+
+# Reproducibility
+
+The `r Biocpkg("chevreuldata")` package `r Citep(bib[["chevreuldata"]])` was made possible thanks to:
+
+* R `r Citep(bib[["R"]])`
+* `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
+* `r CRANpkg("knitr")` `r Citep(bib[["knitr"]])`
+* `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`
+* `r CRANpkg("rmarkdown")` `r Citep(bib[["rmarkdown"]])`
+* `r CRANpkg("sessioninfo")` `r Citep(bib[["sessioninfo"]])`
+* `r CRANpkg("testthat")` `r Citep(bib[["testthat"]])`
+
+This package was developed using `r BiocStyle::Biocpkg("biocthis")`.
+
+
+Code for creating the vignette
+
+```{r createVignette, eval=FALSE}
+## Create the vignette
+library("rmarkdown")
+system.time(render("human_gene_transcript_sce.Rmd", "BiocStyle::html_document"))
+
+## Extract the R code
+library("knitr")
+knit("human_gene_transcript_sce.Rmd", tangle = TRUE)
+```
+
+Date the vignette was generated.
+
+```{r reproduce1, echo=FALSE}
+## Date the vignette was generated
+Sys.time()
+```
+
+Wallclock time spent generating the vignette.
+
+```{r reproduce2, echo=FALSE}
+## Processing time in seconds
+totalTime <- diff(c(startTime, Sys.time()))
+round(totalTime, digits = 3)
+```
+
+`R` session information.
+
+```{r reproduce3, echo=FALSE}
+## Session info
+library("sessioninfo")
+options(width = 120)
+session_info()
+```
+
+
+
+# Bibliography
+
+This vignette was generated using `r Biocpkg("BiocStyle")` `r Citep(bib[["BiocStyle"]])`
+with `r CRANpkg("knitr")` `r Citep(bib[["knitr"]])` and `r CRANpkg("rmarkdown")` `r Citep(bib[["rmarkdown"]])` running behind the scenes.
+
+Citations made with `r CRANpkg("RefManageR")` `r Citep(bib[["RefManageR"]])`.
+
+```{r vignetteBiblio, results = "asis", echo = FALSE, warning = FALSE, message = FALSE}
+## Print bibliography
+PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))
+```