diff --git a/vignettes/dataset-investigation.qmd b/vignettes/dataset-investigation.qmd deleted file mode 100644 index 14b4aa4..0000000 --- a/vignettes/dataset-investigation.qmd +++ /dev/null @@ -1,81 +0,0 @@ ---- -title: "Dataset investigation: What to do when you get your data" -format: html -minimal: true -vignette: > - %\VignetteIndexEntry{Dataset investigation: What to do when you get your data} - %\VignetteEngine{quarto::html} - %\VignetteEncoding{UTF-8} -knitr: - opts_chunk: - collapse: true - comment: '#>' ---- - -## In Construction - -```{r} -library(knitr) -library(quarto) -#knitr::opts_knit$set(root.dir = './') -``` - -# Introduction - -So, you (or your amazing lab mate) have finally finished the data acquisition, -and now you have a dataset in hand. What's next? Unfortunately, the work isn't -over yet. Before diving into any analysis, it's crucial to understand the -dataset itself. This is the first step in any data analysis workflow, ensuring -that the data is of good quality and is well-prepared for preprocessing and any -downstream analysis you plan to perform. - -In this vignette, we present the dataset used throughout the different vignettes -of this website. It's far from a *perfect* dataset, which actually mirrors the -reality of most datasets you'll encounter in research. - -Some issues will indeed be specific to this described dataset. However, the -purpose of this vignette is to encourage you to think critically about your data -and guide you through steps that can help you avoid spending hours on an -analysis, only to realize later that some samples or features should have been -removed or flagged earlier on. - -# Dataset Description - -In this workflow, two datasets are used: - -1. An LC-MS-based (MS1 level only) untargeted metabolomics dataset to quantify - small polar metabolites in human plasma samples. -2. An additional LC-MS/MS dataset of selected samples from the former study for - the identification and annotation of significant features. - -The samples were randomly selected from a larger study aimed at identifying -metabolites with varying abundances between individuals suffering from -cardiovascular disease (CVD) and healthy controls (CTR). The subset analyzed -here includes data for three CVD patients, three CTR individuals, and four -quality control (QC) samples. The QC samples, representing a pooled serum sample -from a large cohort, were measured repeatedly throughout the experiment to -monitor signal stability. - -The data and metadata for this workflow are available on the MetaboLights -database under the ID: MTBLS8735. - -The detailed materials and methods used for the sample analysis are also -available in the MetaboLights entry. This is particularly important for -understanding the analysis and the parameters used. It should be noted that the -samples were analyzed using ultra-high-performance liquid chromatography (UHPLC) -coupled to a Q-TOF mass spectrometer (TripleTOF 5600+), and chromatographic -separation was achieved using hydrophilic interaction liquid chromatography -(HILIC). - -- Consider moving visualizations from the end-to-end vignette to here for a - clearer understanding of the dataset. -- Provide more in-depth visualizations to explore and understand the dataset - quality. -- Compare pool lc-ms and pool lc-ms/ms and show that we have better separation - on the second run. - -```{r} -getwd() -list.files() -list.dirs() -``` diff --git a/vignettes/quarto.qmd b/vignettes/quarto.qmd new file mode 100644 index 0000000..8a9fcf9 --- /dev/null +++ b/vignettes/quarto.qmd @@ -0,0 +1,101 @@ +--- +title: quarto vignettes +description: > + Learn how quarto vignettes work with pkgdown, including currently supported + features and known limitations. +vignette: > + %\VignetteIndexEntry{quarto vignettes} + %\VignetteEngine{quarto::html} + %\VignetteEncoding{UTF-8} +knitr: + opts_chunk: + collapse: true + comment: '#>' +--- + +pkgdown effectively uses quarto only to generate HTML and then supplies its own +CSS and JS. This means that when quarto introduces new features, pkgdown may lag +behind in their support. If you're trying out something that doesn't work (and +isn't mentioned explicitly below), please [file an +issue](https://github.com/r-lib/pkgdown/issues) so we can look into it. + + +## Operation + +pkgdown turns your articles directory into a quarto project by temporarily +adding a `_quarto.yml` to your articles. You can also add your own if you want +to control options for all quarto articles. If you do so, and you have a mix of +`.qmd` and `.Rmd` files, you'll need to include the following yaml so that +RMarkdown can continue to handle the .Rmd files: + + +```yaml +project: + render: ['*.qmd'] +``` + +### GitHub Actions + +The `setup-r-dependencies` action will +[automatically](https://github.com/r-lib/actions/tree/v2-branch/setup-r-dependencies#usage) +install Quarto in your GitHub Actions if a .qmd file is present in your +repository (see the `install-quarto` parameter for more details). + + + +## Limitations + +* Callouts are not currently supported + (). + +* pkgdown assumes that you're using [quarto vignette + style](https://quarto-dev.github.io/quarto-r/articles/hello.html), or more + generally an html format with [`minimal: + true`](https://quarto.org/docs/output-formats/html-basics.html#minimal-html). Specifically, + only HTML vignettes are currently supported. + +* You can't customise mermaid styles with quarto mermaid themes. If you want to + change the colours, you'll need to provide your own custom CSS as shown in + [the quarto + docs](https://quarto.org/docs/authoring/diagrams.html#customizing-mermaid). + +* pkgdown will pass the `lang` setting on to quarto, but the set of available + language is not perfectly matched. Learn more in + , including how to supply + your own translations. + + +## Supported features + +The following sections demonstrate a bunch of useful quarto features so that we +can make sure that they work. + +### Inline formatting + +* [Small caps]{.smallcaps} + +* Here is a footnote reference[^1] + +[^1]: And here is the footnote. + +### Code + +```{r} +#| fig.alt: A plot of the numbers 1, 2, and 3 +1 + 1 +2 + 2 + +plot(1:3) +``` + +## To do + +* [ ] Code annotations +* [ ] Tabsets +* [x] Citations +* [x] Task/to do lists +* [x] Figures +* [x] Equations +* [x] Cross-references +* [x] Footnotes +* [x] Callouts