Merge pull request #142 from selkamand/joss_prereview

Joss prereview

.Rbuildignore

@@ -10,3 +10,4 @@
 ^Meta$
 ^codecov\.yml$
 ^paper
+CONTRIBUTING.md

CONTRIBUTING.md

@@ -0,0 +1,74 @@
+### Contribute to the Software
+
+There are many ways to contribute to ggoncoplot.
+
+1.  Request features you would like to by [creating new issues on
+    github](https://github.com/selkamand/ggoncoplot/issues)
+2.  [Make your visualisation packages ggoncoplot-compatible]
+3.  [Directly contribute to the ggoncoplot codebase]
+
+#### Make your visualisation packages ggoncoplot-compatible
+
+If your package produces ggplots that you would like to interactively
+link with ggoncoplot, consider converting your geoms to their ggiraph
+interactive equivalents and adding a data_id based on a sample
+identifier column in the dataset. That way end-users can create a
+data-linked oncoplot composed with your packages plots using patchwork
+([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages))
+
+#### Directly contribute to the ggoncoplot codebase
+
+We welcome contributions from the community to enhance and expand the
+functionality of `ggoncoplot`. Whether you want to fix a bug, add new
+features, improve documentation, or optimize performance, your efforts
+are highly valued. To get started:
+
+1.  **Fork the Repository**: Click on the 'Fork' button at the top right
+    of this page to create a copy of the repository in your GitHub
+    account.
+
+2.  **Clone the Repository**: Use `git clone` to clone your forked
+    repository to your local machine.
+
+    ``` bash
+    git clone https://github.com/selkamand/ggoncoplot.git
+    ```
+
+3.  **Create a Branch**
+
+    ``` bash
+    git checkout -b feature-name
+    ```
+
+4.  **Make Changes**: Implement your changes in the new branch
+
+5.  **Commit and Push**: Commit your changes and push the branch to your
+    forked repository.
+
+6.  **Create a Pull Request**: Go to the original repository and open a
+    pull request from your branch. Please provide a clear description of
+    your changes and any relevant issues or discussions.
+
+### Report Issues or Problems with the Software
+
+If you encounter any issues, bugs, or have suggestions for improvements,
+please report them using the [GitHub Issues Tab](https://github.com/selkamand/ggoncoplot/issues/).
+
+### Seek Support
+
+For any questions or support regarding the use of ggoncoplot you can:
+
+-   **Check the Documentation**: Comprehensive documentation is
+    available [here](https://selkamand.github.io/ggoncoplot/index.html).
+
+-   **Create a** [new
+    issue](https://github.com/selkamand/ggoncoplot/issues/new) with your
+    query.
+
+-   **Browse Existing Issues**: Check the
+    [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see
+    if your query has been addressed.
+
+-   **Contact Us**: If you need direct assistance, please [contact the
+    maintainers
+    directly](mailto:[email protected]?subject=ggoncoplot)

README.Rmd

@@ -140,77 +140,5 @@ during the early stages of ggoncoplot development.
 
 ## Community Contributions
 
-### Contribute to the Software
+All types of contributions are encouraged and valued. See our [guide to community contributions](CONTRIBUTING.md) for different ways to help.
 
-There are many ways to contribute to ggoncoplot.
-
-1.  Request features you would like to by [creating new issues on
-    github](https://github.com/selkamand/ggoncoplot/issues)
-2.  [Make your visualisation packages ggoncoplot-compatible]
-3.  [Directly contribute to the ggoncoplot codebase]
-
-#### Make your visualisation packages ggoncoplot-compatible
-
-If your package produces ggplots that you would like to interactively
-link with ggoncoplot, consider converting your geoms to their ggiraph
-interactive equivalents and adding a data_id based on a sample
-identifier column in the dataset. That way end-users can create a
-data-linked oncoplot composed with your packages plots using patchwork
-([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages))
-
-#### Directly contribute to the ggoncoplot codebase
-
-We welcome contributions from the community to enhance and expand the
-functionality of `ggoncoplot`. Whether you want to fix a bug, add new
-features, improve documentation, or optimize performance, your efforts
-are highly valued. To get started:
-
-1.  **Fork the Repository**: Click on the 'Fork' button at the top right
-    of this page to create a copy of the repository in your GitHub
-    account.
-
-2.  **Clone the Repository**: Use `git clone` to clone your forked
-    repository to your local machine.
-
-    ``` bash
-    git clone https://github.com/selkamand/ggoncoplot.git
-    ```
-
-3.  **Create a Branch**
-
-    ``` bash
-    git checkout -b feature-name
-    ```
-
-4.  **Make Changes**: Implement your changes in the new branch
-
-5.  **Commit and Push**: Commit your changes and push the branch to your
-    forked repository.
-
-6.  **Create a Pull Request**: Go to the original repository and open a
-    pull request from your branch. Please provide a clear description of
-    your changes and any relevant issues or discussions.
-
-### Report Issues or Problems with the Software
-
-If you encounter any issues, bugs, or have suggestions for improvements,
-please report them using the [GitHub Issues Tab](https://github.com/selkamand/ggoncoplot/issues/).
-
-### Seek Support
-
-For any questions or support regarding the use of ggoncoplot you can:
-
--   **Check the Documentation**: Comprehensive documentation is
-    available [here](https://selkamand.github.io/ggoncoplot/index.html).
-
--   **Create a** [new
-    issue](https://github.com/selkamand/ggoncoplot/issues/new) with your
-    query.
-
--   **Browse Existing Issues**: Check the
-    [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see
-    if your query has been addressed.
-
--   **Contact Us**: If you need direct assistance, please [contact the
-    maintainers
-    directly](mailto:[email protected]?subject=ggoncoplot)

README.md

@@ -172,79 +172,5 @@ during the early stages of ggoncoplot development.
 
 ## Community Contributions
 
-### Contribute to the Software
-
-There are many ways to contribute to ggoncoplot.
-
-1.  Request features you would like to by [creating new issues on
-    github](https://github.com/selkamand/ggoncoplot/issues)
-2.  [Make your visualisation packages
-    ggoncoplot-compatible](#make-your-visualisation-packages-ggoncoplot-compatible)
-3.  [Directly contribute to the ggoncoplot
-    codebase](#directly-contribute-to-the-ggoncoplot-codebase)
-
-#### Make your visualisation packages ggoncoplot-compatible
-
-If your package produces ggplots that you would like to interactively
-link with ggoncoplot, consider converting your geoms to their ggiraph
-interactive equivalents and adding a data_id based on a sample
-identifier column in the dataset. That way end-users can create a
-data-linked oncoplot composed with your packages plots using patchwork
-([example](https://selkamand.github.io/ggoncoplot/articles/manual.html#interaction-with-other-packages))
-
-#### Directly contribute to the ggoncoplot codebase
-
-We welcome contributions from the community to enhance and expand the
-functionality of `ggoncoplot`. Whether you want to fix a bug, add new
-features, improve documentation, or optimize performance, your efforts
-are highly valued. To get started:
-
-1.  **Fork the Repository**: Click on the ‘Fork’ button at the top right
-    of this page to create a copy of the repository in your GitHub
-    account.
-
-2.  **Clone the Repository**: Use `git clone` to clone your forked
-    repository to your local machine.
-
-    ``` bash
-    git clone https://github.com/selkamand/ggoncoplot.git
-    ```
-
-3.  **Create a Branch**
-
-    ``` bash
-    git checkout -b feature-name
-    ```
-
-4.  **Make Changes**: Implement your changes in the new branch
-
-5.  **Commit and Push**: Commit your changes and push the branch to your
-    forked repository.
-
-6.  **Create a Pull Request**: Go to the original repository and open a
-    pull request from your branch. Please provide a clear description of
-    your changes and any relevant issues or discussions.
-
-### Report Issues or Problems with the Software
-
-If you encounter any issues, bugs, or have suggestions for improvements,
-please report them using the [GitHub Issues
-Tab](https://github.com/selkamand/ggoncoplot/issues/).
-
-### Seek Support
-
-For any questions or support regarding the use of ggoncoplot you can:
-
-- **Check the Documentation**: Comprehensive documentation is available
-  [here](https://selkamand.github.io/ggoncoplot/index.html).
-
-- **Create a** [new
-  issue](https://github.com/selkamand/ggoncoplot/issues/new) with your
-  query.
-
-- **Browse Existing Issues**: Check the
-  [Issues](https://github.com/selkamand/ggoncoplot/issues) page to see
-  if your query has been addressed.
-
-- **Contact Us**: If you need direct assistance, please [contact the
-  maintainers directly](mailto:[email protected]?subject=ggoncoplot)
+All types of contributions are encouraged and valued. See our [guide to
+community contributions](CONTRIBUTING.md) for different ways to help.

paper/jats/paper.jats

@@ -313,6 +313,7 @@ a Creative Commons Attribution 4.0 International License (CC BY
       <article-title>Ggiraph: Make ’ggplot2’ graphics interactive</article-title>
       <year iso-8601-date="2024">2024</year>
       <uri>https://davidgohel.github.io/ggiraph/</uri>
+      <pub-id pub-id-type="doi">10.32614/CRAN.package.ggiraph</pub-id>
     </element-citation>
   </ref>
   <ref id="ref-pedersenU003A2024">
@@ -323,6 +324,7 @@ a Creative Commons Attribution 4.0 International License (CC BY
       <article-title>Patchwork: The composer of plots</article-title>
       <year iso-8601-date="2024">2024</year>
       <uri>https://patchwork.data-imaginist.com</uri>
+      <pub-id pub-id-type="doi">10.32614/cran.package.patchwork</pub-id>
     </element-citation>
   </ref>
   <ref id="ref-wickhamU003A2016">
@@ -335,6 +337,7 @@ a Creative Commons Attribution 4.0 International License (CC BY
       <year iso-8601-date="2016">2016</year>
       <isbn>978-3-319-24277-4</isbn>
       <uri>https://ggplot2.tidyverse.org</uri>
+      <pub-id pub-id-type="doi">10.32614/CRAN.package.ggplot2</pub-id>
     </element-citation>
   </ref>
   <ref id="ref-goldmanU003A2020">

paper/paper.bib

@@ -45,15 +45,17 @@ @misc{gohel:2024
   author = {David Gohel and Panagiotis Skintzos},
   year = {2024},
   note = {R package version 0.8.10},
-  url = {https://davidgohel.github.io/ggiraph/}
+  url = {https://davidgohel.github.io/ggiraph/},
+  doi = {10.32614/CRAN.package.ggiraph}
 }
 
 @misc{pedersen:2024,
   title = {patchwork: The Composer of Plots},
   author = {Thomas Lin Pedersen},
   year = {2024},
   note = {R package version 1.2.0.9000},
-  url = {https://patchwork.data-imaginist.com}
+  url = {https://patchwork.data-imaginist.com},
+  doi = {10.32614/cran.package.patchwork}
 }
 
 @Book{wickham:2016,
@@ -63,6 +65,7 @@ @Book{wickham:2016
   year = {2016},
   isbn = {978-3-319-24277-4},
   url = {https://ggplot2.tidyverse.org},
+  doi = {10.32614/CRAN.package.ggplot2}
 }