Improve and reorganize documentation: new vignettes, navbar dropdown,…

.Rbuildignore

@@ -7,3 +7,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^doc$
+^Meta$

.github/workflows/pkgdown.yaml

@@ -34,6 +34,11 @@ jobs:
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
+
+      - name: Manually install newer version of preprocessCore
+        run: |
+          Rscript -e "pak::pkg_install('BiocManager')"
+          Rscript -e "BiocManager::install('preprocessCore', configure.args = c(preprocessCore = '--disable-threading'), force= TRUE, update=TRUE, type = 'source')"
 
       - name: Build site
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)

.gitignore

@@ -5,3 +5,5 @@
 .DS_Store
 .Rproj
 docs
+/doc/
+/Meta/

_pkgdown.yml

@@ -2,3 +2,30 @@ url: http://omnideconv.org/methylDeconv/
 template:
   bootstrap: 5
 
+articles:
+  - title: "Getting Started"
+    contents:
+      - getting_started
+      - visualization
+  - title: "Contributing"
+    contents:
+      - contribute
+
+navbar:
+  structure:
+    left:
+      - home
+      - reference
+      - articles
+      - news
+  components:
+    articles:
+      text: "Articles"
+      menu:
+        - text: "Getting Started"
+          href: articles/getting_started.html
+        - text: "Visualization"
+          href: articles/visualization.html
+        - text: "Contribute"
+          href: articles/contribute.html
+

vignettes/contribute.R

@@ -0,0 +1 @@
+

vignettes/contribute.Rmd

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+---
+title: "Contribute: Adding a New Method to methyldeconv"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Contribute: Adding a New Method to methyldeconv}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+# Contributing a New Method to methyldeconv
+
+Thank you for your interest in contributing to **methyldeconv**! This guide will help you add a new cell-type deconvolution method to the package.
+
+## 1. Fork and Clone the Repository
+
+- Fork the [methyldeconv GitHub repository](https://github.com/omnideconv/methyldeconv).
+- Clone your fork locally and create a new branch for your feature.
+
+## 2. Add Your Method Implementation
+
+- Add a new R script for your method in the `R/` directory (e.g., `mynewmethod.R`).
+- Follow the structure of existing methods (see files like `epidish.R`, `houseman.R`, etc.).
+- Your function should:
+    - Accept a beta matrix or methylSet as input.
+    - Return results in a format consistent with other methods (see `run_epidish`, `run_houseman`, etc.).
+    - Include roxygen2 documentation.
+
+## 3. Register Your Method
+
+- If your method should be accessible via the unified interface (`deconvolute` or `deconvolute_combined`), update the relevant logic in `main.R`.
+- Add your method to the list of supported methods and document any new parameters.
+
+## 4. Expose All Method Parameters via methyldeconv
+
+To ensure users can fully utilize your new method, make sure that all relevant parameters of your function are accessible through the main methyldeconv interfaces (`deconvolute` and/or `deconvolute_combined`).
+
+- Update the argument handling in `main.R` so that users can pass any method-specific parameters when calling these functions.
+- Clearly document these parameters in your function's roxygen2 documentation and in the main interface documentation if needed.
+- This approach ensures flexibility and makes your method as useful as possible for a wide range of use cases.
+
+## 5. Document Your Method
+
+- Add a roxygen2 documentation block to your function.
+- Run `devtools::document()` to update the manual files in `man/`.
+- Optionally, add an example to the README or a new vignette.
+
+## 6. Add Tests
+
+- Add tests for your method in `tests/testthat/` (see `test_methods.R` for examples).
+- Ensure your method is covered by the test suite.
+
+## 7. Check and Build
+
+- Run `devtools::check()` to ensure your changes pass all checks.
+- Build the documentation site locally with `pkgdown::build_site()` to preview your changes.
+
+## 8. Submit a Pull Request
+
+- Push your branch to your fork and open a pull request against the main repository.
+- Describe your changes and reference any related issues.
+
+## 9. Code Review
+
+- Address any feedback or requested changes from the maintainers.
+
+---
+
+For more details, see the [pkgdown documentation](https://pkgdown.r-lib.org/) and the [R packages book](https://r-pkgs.org/).
+
+If you have questions, feel free to open an issue or ask for help in your pull request!