Merge pull request #132 from selkamand/127-add-community-contribution…

…s-section-to-readme

127 add community contributions section to readme

README.Rmd

@@ -1,5 +1,8 @@
 ---
 output: github_document
+editor_options: 
+  markdown: 
+    wrap: 72
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -13,20 +16,27 @@ knitr::opts_chunk$set(
 )
 ```
 
-# ggoncoplot <a href="https://selkamand.github.io/ggoncoplot/"><img src="man/figures/logo.png" align="right" height="104" /></a>
+# ggoncoplot <a href="https://selkamand.github.io/ggoncoplot/"><img src="man/figures/logo.png" align="right" height="104"/></a>
 
 <!-- badges: start -->
 
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![CRAN status](https://www.r-pkg.org/badges/version/ggoncoplot)](https://CRAN.R-project.org/package=ggoncoplot)
-[![Codecov test coverage](https://codecov.io/gh/selkamand/ggoncoplot/branch/master/graph/badge.svg)](https://app.codecov.io/gh/selkamand/ggoncoplot?branch=master)
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/ggoncoplot)](https://CRAN.R-project.org/package=ggoncoplot)
+[![Codecov test
+coverage](https://codecov.io/gh/selkamand/ggoncoplot/branch/master/graph/badge.svg)](https://app.codecov.io/gh/selkamand/ggoncoplot?branch=master)
 [![R-CMD-check](https://github.com/selkamand/ggoncoplot/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/selkamand/ggoncoplot/actions/workflows/R-CMD-check.yaml)
-![GitHub Issues or Pull Requests](https://img.shields.io/github/issues-closed/selkamand/ggoncoplot)
+![GitHub Issues or Pull
+Requests](https://img.shields.io/github/issues-closed/selkamand/ggoncoplot)
 [![](https://img.shields.io/github/languages/code-size/selkamand/ggoncoplot.svg)](https://github.com/selkamand/ggoncoplot)
-![GitHub last commit](https://img.shields.io/github/last-commit/selkamand/ggoncoplot)
+![GitHub last
+commit](https://img.shields.io/github/last-commit/selkamand/ggoncoplot)
 
 <!-- badges: end -->
 
-**ggoncoplot** creates interactive oncoplots from mutation level datasets
+**ggoncoplot** creates interactive oncoplots from mutation level
+datasets
 
 ## Installation
 
@@ -38,22 +48,26 @@ remotes::install_github('selkamand/ggoncoplot')
 
 ## Usage
 
-For complete usage, see [manual](https://selkamand.github.io/ggoncoplot/articles/manual.html)
+For complete usage, see
+[manual](https://selkamand.github.io/ggoncoplot/articles/manual.html)
 
 ### Input
 
-The input for ggoncoplot is a data.frame with 1 row per mutation in cohort and columns describing the following:
+The input for ggoncoplot is a data.frame with 1 row per mutation in
+cohort and columns describing the following:
 
-- Gene Symbol
+-   Gene Symbol
 
-- Sample Identifier 
+-   Sample Identifier
 
-- (optional) mutation type
+-   (optional) mutation type
 
-- (optional) tooltip (character string: what we show on mouse hover over a particular mutation)
+-   (optional) tooltip (character string: what we show on mouse hover
+    over a particular mutation)
 
-
-These columns can be in any order, and named anything. You define the mapping of your input dataset columns to the required features in the call to **ggoncoplot**
+These columns can be in any order, and named anything. You define the
+mapping of your input dataset columns to the required features in the
+call to **ggoncoplot**
 
 ### Basic Example
 
@@ -74,7 +88,6 @@ gbm_df |>
   )
 ```
 
-
 ### Add marginal plots
 
 ```{r fig.height=6, fig.width=12}
@@ -110,14 +123,94 @@ gbm_df |>
   )
 ```
 
-
 ## Acknowledgements
 
-We acknowledge the developers and contributors whose packages and efforts were integral to the development of ggoncoplot:
+We acknowledge the developers and contributors whose packages and
+efforts were integral to the development of ggoncoplot:
+
+-   **David Gohel** for the `ggiraph` package, which enables the
+    interactivity of ggoncoplot.
+-   **Thomas Lin Pedersen** for his contributions to the `patchwork`
+    package and the maintenance of `ggplot2`.
+-   **Hadley Wickham** and all contributors to the `ggplot2` package,
+    which provides a robust foundation for data visualization in R.
+
+Additionally, we thank **Dr. Marion Mateos** for her insightful feedback
+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]
+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).
 
-- **David Gohel** for the `ggiraph` package, which enables the interactivity of ggoncoplot.
-- **Thomas Lin Pedersen** for his contributions to the `patchwork` package and the maintenance of `ggplot2`.
-- **Hadley Wickham** and all contributors to the `ggplot2` package, which provides a robust foundation for data visualization in R.
+-   **Create a** [new
+    issue](https://github.com/selkamand/ggoncoplot/issues/new) with your
+    query.
 
-Additionally, we thank **Dr. Marion Mateos** for her insightful feedback during the early stages of ggoncoplot development.
+-   **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

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# ggoncoplot <a href="https://selkamand.github.io/ggoncoplot/"><img src="man/figures/logo.png" align="right" height="104" /></a>
+# ggoncoplot <a href="https://selkamand.github.io/ggoncoplot/"><img src="man/figures/logo.png" align="right" height="104"/></a>
 
 <!-- badges: start -->
 
@@ -142,6 +142,15 @@ gbm_df |>
 #> ✔ Mutation Types are described using valid MAF terms ... using MAF palete
 #> ! TMB plot: Ignoring `col_mutation_type` since `log10_transform = TRUE`.
 #> This is because you cannot accurately plot stacked bars on a logarithmic scale
+#> 
+#> ── Plotting Sample Metadata ────────────────────────────────────────────────────
+#> ! Categorical columns must have <= 6 unique values to be visualised. Columns with too many unique values:  (20),  (388), and  (388)
+#> 
+#> ── Sorting
+#> ℹ Sorting X axis by: Order of appearance
+#> 
+#> ── Generating Plot
+#> ℹ Found 4 plottable columns in data
 ```
 
 <img src="man/figures/README-unnamed-chunk-4-1.png" width="100%" />
@@ -160,3 +169,82 @@ efforts were integral to the development of ggoncoplot:
 
 Additionally, we thank **Dr. Marion Mateos** for her insightful feedback
 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)