Merge pull request #1 from rformassspectrometry/phili

addition of vignettes and change website setup

.gitignore

@@ -5,4 +5,5 @@ local_data
 /.quarto/
 /_site/
 *.png
-*.html
+*.html
+*.RData

DESCRIPTION

@@ -47,4 +47,4 @@ BugReports: https://github.com/rformassspectrometry/metabonaut/issues/new
 VignetteBuilder: knitr
 BiocType: Workflow
 RoxygenNote: 7.3.2
-DockerImage: rformassspectrometry/metabonaut
+DockerImage: rformassspectrometry/metabonaut:latest

NEWS.md

@@ -1,4 +1,10 @@
-# metabonaut 0.0.1
+# metabonaut 0.0.2
+
+## Changes in 0.0.2
+- Switch to Quarto instead of Rmarkdown
+- Addition of Alignment to reference dataset vignette
+- Addition of the Data investigation vignette 
+- Addition of the Install vignette
 
 ## Changes in 0.0.1
 - Addition of basic files for a workflow package.

README.md

@@ -1,99 +1,60 @@
-# Exploring and analyzing untargeted metabolomics data
+# Exploring and Analyzing Untargeted Metabolomics Data
 
 [![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)
 
+Welcome to **Metabonaut**! :astronaut:
 
-Welcome to Metabonaut ! :astronaut:
-
-This initiative present a series of workflows based on a small LC-MS/MS dataset
-using R and Bioconductor packages. Throughout the workflows, we demonstrate how 
-the various algorithms can be adapted to the particular data set and how various
-R packages can be seamlessly integrated to ensure efficient and reproducible 
-processing. 
-
-The main workflow presented is the ["Complete end-to-end LC-MS/MS Metabolomic
-Data analysis"](https://rformassspectrometry.github.io/metabonaut/articles/end-to-end-untargeted-metabolomics.html) 
-
-The full R code of all examples along with comprehensive descriptions is
-provided in the [end-to-end-untargeted-metabolomics.Rmd](./vignettes/end-to-end-untargeted-metabolomics.Rmd)
-file. This file can be opened with e.g. RStudio which allows execution of the
-individual R commands (see section below for additionally required R
-packages). The R command `rmarkdown::render("xcms-preprocessing.Rmd")` would
-generate the html file
-[xcms-preprocessing.html](https://github.com/rformassspectrometry/metabonaut/end-to-end-untargeted-metabolomics.html).
-
-## Important to note 
-
-This tutorial expect a user that has some basic knowledge of R and Rmarkdown. 
-We would advise to go through a short tutorial for each in order to be 
-comfortable testing the code and easily adapting it to your own data. For Rmarkdown, 
-click [here](https://bookdown.org/yihui/rmarkdown/) for R, [here](https://learn-r.org/) and [here](https://swirlstats.com/students.html) 
-you can find a really fun way to learn basic R programming through an interactive short course
-
-## Installation
-
-The workshop files along with an R runtime environment including all required
-packages and the RStudio (Posit) editor are all bundled in a *docker*
-container. After installation, this docker container can be run on the computer
-and the code and examples from the workshop can be evaluated within this
-environment (without the need to install any additional packages or files).
-
-This version of the workshop uses packages from **Bioconductor devel**
- and hence bases on Bioconductor's docker container with the development version of the 
- packages. A more stable version will come soon.
- The required steps for installation are:
-
-- If you don't already have, install [docker](https://www.docker.com/). Find
-  installation information [here](https://docs.docker.com/desktop/).
-- Get the [docker image](https://hub.docker.com/r/rformassspectrometry/metabonaut) of
-  this tutorial e.g. from the command line with `docker pull
-  rformassspectrometry/metabonaut:latest`.
-- Start the docker container, either through the Docker Desktop, or on the
-  command line with
-```
-  docker run \
-      -e PASSWORD=bioc \
-      -p 8787:8787 \
-      rformassspectrometry/metabonaut:latest
-```
-
-- Enter `http://localhost:8787` in a web browser and log in with username
-  `rstudio` and password `bioc`.
-- In the RStudio server version: open any of the R-markdown (*.Rmd*) files in
-  the *vignettes* folder and evaluate the R code blocks in that document.
-
-For manual installation, an R version >= 4.4.0 is required as well as recent
-versions of the packages used in the workflow.
-
-For now 2 packages used in this workflow are not on bioconductor and therefore need to be
-downloaded from github.
-Run the code as follow: 
-
-```r
-install.packages("BiocManager")
-BiocManager::install(c('RCurl', 'xcms', 'MsExperiment', 'SummarizedExperiment',
-    'Spectra', 'MetaboCoreUtils', 'limma', 'matrixStats', 'pander', 
-    'RColorBrewer', 'pheatmap', 'vioplot', 'ggfortify', 'gridExtra', 
-    'AnnotationHub', 'CompoundDb', 'MetaboAnnotation', 
-    'RforMassSpectrometry/MsIO', 'RforMassSpectrometry/MsBackendMetaboLights'), 
-ask = FALSE, dependencies = TRUE)"
-```
-
-## Known issues 
-
-This workflow is still getting ready to be fully deployed, therefore we might have some ongoing issue that we are actively resolving. If we know about them we will list them below.
-
-For now, we are not aware of any problem in the code. If you have any issue be sure to check that you have the latest devel version of all the packages. If the issue is not resolved by the updating of packages then please report it with a reproducible example on github [here](https://github.com/rformassspectrometry/metabonaut/issues)
-
-If you have any other issue, do not hesitate to report them to us. 
+This initiative presents a series of workflows based on a small LC-MS/MS dataset, 
+utilizing R and Bioconductor packages. Throughout these workflows, we demonstrate 
+how to adapt various algorithms to specific datasets and how to seamlessly 
+integrate R packages to ensure efficient, reproducible processing.
 
-## Contribution
+The primary workflow is the 
+["Complete End-to-End LC-MS/MS Metabolomic Data Analysis"](https://rformassspectrometry.github.io/metabonaut/articles/end-to-end-untargeted-metabolomics.html).
+
+The full R code for all examples, along with detailed descriptions, is available 
+in the 
+[end-to-end-untargeted-metabolomics.Rmd](https://rformassspectrometry.github.io/metabonaut/vignettes/end-to-end-untargeted-metabolomics.Rmd) 
+file. This file can be opened in RStudio, allowing you to execute each individual 
+R command (see the section below for additional required R packages).
+
+Other vignettes on this website are interlinked, and you can find a detailed 
+description of the dataset used throughout 
+[here](https://rformassspectrometry.github.io/metabonaut/articles/dataset-investigation.html).
+
+We strive for reproducibility. These workflows are designed to remain stable 
+over time, allowing you to run all the vignettes together as one comprehensive 
+"super-vignette."
+
+## Important Notes
+
+The tutorials provided assume that users have basic knowledge of R and RMarkdown. 
+If you're unfamiliar with either, we recommend completing a short tutorial to help 
+you test the code and adapt it to your data. For RMarkdown, click 
+[here](https://bookdown.org/yihui/rmarkdown/). For R, check out 
+[this](https://learn-r.org/) or try an interactive course 
+[here](https://swirlstats.com/students.html) for a fun introduction to basic R 
+programming.
 
-For contributions, see the [RforMassSpectrometry contributions
-guideline](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions).
+## Known Issues
+
+This is just the beginning of our Metabonaut journey, and the website is still 
+being refined. We're actively addressing any ongoing issues. If we're aware of a 
+problem, we'll list it below.
+
+Currently, there are no known issues with the code. If you encounter any, please 
+ensure you have the latest versions of all required packages (as detailed above). 
+If the issue persists, please report it with a reproducible example on GitHub 
+[here](https://github.com/rformassspectrometry/metabonaut/issues).
+
+If you encounter any other issues, don't hesitate to let us know!
+
+## Contribution
 
+For contributions, please see the 
+[RforMassSpectrometry contributions guideline](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions).
 
 ## Code of Conduct
 
-See the [RforMassSpectrometry Code of
-Conduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#code-of-conduct).
+Please review the 
+[RforMassSpectrometry Code of Conduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#code-of-conduct).

_pkgdown.yml

@@ -1,4 +1,24 @@
 url: https://rformassspectrometry.github.io/metabonaut/
 template:
   bootstrap: 5
+  bootswatch: flatly
+ light-switch: true
 
+navbar:
+  title: "Metabonaut"
+  left: 
+    - text: "Install"
+      href: articles/install_v0.html
+    - text: "Vignettes"
+      menu: 
+        - text: "Dataset investigation: What to do when you get your data"
+          href: articles/dataset-investigation.html
+        - text: "End-to-end workflow for untargeted metabolomics data analysis in R"
+          href: articles/end-to-end-untargeted-metabolomics.html
+        - text: "Seamless Alignment: Merging New data with Existing Preprocessed Datasets"
+          href: articles/alignment-to-external-dataset.html
+  right:
+  - icon: fa-home
+    href: ../
+  - icon: fa-github
+    href: https://github.com/rformassspectrometry/metabonaut/