Update chunk labels in vignettes (#310)

Author: LouiseDck

vignettes/anndataR.Rmd

@@ -13,7 +13,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r options, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
@@ -34,14 +34,14 @@ This package differs from [**{zellkonverter}**](https://bioconductor.org/package
 
 Install using either **{BiocManager}** or from GitHub using **{pak}**:
 
-```{r, eval = FALSE}
+```{r install-BiocManager, eval = FALSE}
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
   install.packages("BiocManager")
 }
 BiocManager::install("anndataR")
 ```
 
-```{r, eval = FALSE}
+```{r install-pak, eval = FALSE}
 if (!require("pak", quietly = TRUE)) {
   install.packages("pak")
 }
@@ -54,7 +54,7 @@ Here's a quick example of how to use **{anndataR}**.
 
 First, we fetch an example `.h5ad` file included in the package:
 
-```{r}
+```{r h5ad-path}
 library(anndataR)
 
 h5ad_path <- system.file("extdata", "example.h5ad", package = "anndataR")
@@ -169,6 +169,6 @@ write_h5ad(obj, tmpfile)
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```

vignettes/development_status.Rmd

@@ -9,7 +9,7 @@ vignette: >
 
 The following tables show the status of the implementation of each feature in the package:
 
-```{r include=FALSE}
+```{r impl-table, include=FALSE}
 library(tibble)
 library(knitr)
 library(rprojroot)
@@ -132,7 +132,7 @@ status_formatted <- status |>
 
 ## Objects
 
-```{r echo=FALSE, results="asis"}
+```{r impl-table-objects, echo=FALSE, results="asis"}
 # loop over each of the classes and print the table as markdown
 all_classes <- unique(status_formatted$class)
 object_classes <- all_classes[!all_classes %in% c("Seurat", "SingleCellExperiment")]
@@ -152,7 +152,7 @@ for (class_name in object_classes) {
 
 ## Conversion
 
-```{r echo=FALSE, results="asis"}
+```{r impl-table-conversion, echo=FALSE, results="asis"}
 # loop over each of the classes and print the table as markdown
 for (class_name in c("SingleCellExperiment", "Seurat")) {
   cat("### ", class_name, "\n\n", sep = "")
@@ -175,6 +175,6 @@ for (class_name in c("SingleCellExperiment", "Seurat")) {
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```

vignettes/known_issues.Rmd

@@ -9,7 +9,7 @@ vignette: >
 
 This document lists known issues with the package and suggests possible solutions.
 
-```{r echo=FALSE, results="asis"}
+```{r known-issues, echo=FALSE, results="asis"}
 # how to get a file from a package
 data <- yaml::read_yaml(system.file("known_issues.yaml", package = "anndataR"))$known_issues
 
@@ -33,6 +33,6 @@ for (i in seq_along(data)) {
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```

vignettes/software_design.Rmd

@@ -8,7 +8,7 @@ vignette: >
 ---
 
 
-```{r, include = FALSE}
+```{r options, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = ""
@@ -46,6 +46,6 @@ Notation:
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```

vignettes/usage_seurat.Rmd

@@ -8,7 +8,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r options, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -132,6 +132,6 @@ The mapping arguments can also be passed directly to `write_h5ad()`.
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```

vignettes/usage_singlecellexperiment.Rmd

@@ -8,7 +8,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r options, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
@@ -130,6 +130,6 @@ The mapping arguments can also be passed directly to `write_h5ad()`.
 
 ## Session info
 
-```{r}
+```{r sessioninfo}
 sessionInfo()
 ```