Mv enrichment plot

CLAUDE.md

@@ -0,0 +1,30 @@
+# DataFrame
+
+Each specific analysis plot is based on a type from acore `acore.types`. Use the pandera
+schema to validate the input DataFrame.
+
+- use the pandas API whenever you can
+
+## Format
+
+Use black to format the src folder
+
+```bash
+black src
+```
+
+## Ruff checks
+
+```
+ruff check src --fix
+```
+
+## Staging
+
+Ask me if I want to stage the files and provide the command to do so.
+
+## Docstrings
+
+Use the default format for type annotated functions is numpy style.
+
+https://numpydoc.readthedocs.io/en/latest/format.html#parameters

CONTRIBUTING.md

@@ -1,32 +1,33 @@
 # Contributing to VueCore
 
-[VueCore][vuecore-repo] is an **open source project**, and we welcome contributions of all kinds via **GitHub issues** and 
-**pull requests**: correct or improve our [documentation][vuecore-docs], report or fix bugs, propose changes, and 
-implement new features. Please follow these guidelines to make sure that your contribution is easily integrated 
-into the project.
+[VueCore][vuecore-repo] is an **open source project**, and we welcome contributions of all
+kinds via **GitHub issues** and **pull requests**: correct or improve our
+[documentation][vuecore-docs], report or fix bugs, propose changes, and implement new
+features. Please follow these guidelines to make sure that your contribution is easily
+integrated into the project.
 
 ## Contributor Agreement
 
 By contributing, you agree that we may redistribute your work under [our
-license](LICENSE.md). In exchange, we will address your issues and/or assess
-your change proposal as promptly as we can, and help you become a member of our
-community.
+license](LICENSE.md). In exchange, we will address your issues and/or assess your change
+proposal as promptly as we can, and help you become a member of our community.
 
 ## What to Contribute?
 
-The easiest way to get started is by **reporting an issue** that needs to be fixed, 
-such as a bug in the code, unclear explanations, conceptual errors, or other details.
-If you are familiar with Python, Git,, and GitHub, you can **fix the bug** yourself 
-and submit a **pull request (PR)** with your changes, as described below. 
+The easiest way to get started is by **reporting an issue** that needs to be fixed, such
+as a bug in the code, unclear explanations, conceptual errors, or other details. If you
+are familiar with Python, Git,, and GitHub, you can **fix the bug** yourself and submit a
+**pull request (PR)** with your changes, as described below.
 
-You can also contribute by **fixing existing bugs** tagged with the `bug` and 
-`help wanted` labels in the [list of open issues][issues] of the repository. There are 
-**new features and imporvements** tagged with `enhancement` and `help wanted` as well, so
-feel free to start a discussion if you would like to work on one of those. If you come up with 
-any **ideas for new features or improvements** that are not yet reported, we are also happy to hear about them. 
+You can also contribute by **fixing existing bugs** tagged with the `bug` and `help
+wanted` labels in the [list of open issues][issues] of the repository. There are **new
+features and imporvements** tagged with `enhancement` and `help wanted` as well, so feel
+free to start a discussion if you would like to work on one of those. If you come up with
+any **ideas for new features or improvements** that are not yet reported, we are also
+happy to hear about them.
 
-Feedback from beginners is especially valuable, as experienced users may overlook how 
-challenging certain aspects of the software can be for newcomers. Therefore, we encourage 
+Feedback from beginners is especially valuable, as experienced users may overlook how
+challenging certain aspects of the software can be for newcomers. Therefore, we encourage
 you to share any suggestions or observations you have.
 
 ## How to Contribute?
@@ -35,41 +36,44 @@ Here are the ways you can submit your suggestions and contribute to the project:
 
 ### 1. Reporting Issues or Suggesting Improvements
 
-If you have a  [GitHub][github] account (or are willing to [open one][github-join]) but are unfamiliar with 
-Git, you can report bugs or suggest improvements by [creating an issue][new-issue]. This GitHub feature allows 
-for discussion threads on reported issues and proposed enhancements.
+If you have a [GitHub][github] account (or are willing to [open one][github-join]) but
+are unfamiliar with Git, you can report bugs or suggest improvements by [creating an
+issue][new-issue]. This GitHub feature allows for discussion threads on reported issues
+and proposed enhancements.
 
-When reporting an issue, please provide as much relevant information as possible, including:
+When reporting an issue, please provide as much relevant information as possible,
+including:
 
-* A clear and descriptive title
-* A detailed description of the problem or suggestion
-* Steps to reproduce the issue (if applicable)
-* Any relevant screenshots or error messages
-* Your operating system, software version, and additonal details about your local setup that might be helpful in troubleshooting
+- A clear and descriptive title
+- A detailed description of the problem or suggestion
+- Steps to reproduce the issue (if applicable)
+- Any relevant screenshots or error messages
+- Your operating system, software version, and additonal details about your local setup
+  that might be helpful in troubleshooting
 
-> [!TIP]
-> This guide from the [GitHub Docs][github-docs] provides useful tips on [how to write an issue][issue-github-guide].
+> [!TIP] This guide from the [GitHub Docs][github-docs] provides useful tips on [how to
+> write an issue][issue-github-guide].
 
 ### 2. Submitting Changes via Pull Requests (PR)
 
-If you are comfortable using Git/GitHub and would like to add or modify a functionality, you can submit a **PR**. 
-You may want to look at [How to Contribute to an Open Source Project on GitHub][how-contribute]. 
-In brief, we use [GitHub flow][github-flow] to manage changes:
+If you are comfortable using Git/GitHub and would like to add or modify a functionality,
+you can submit a **PR**. You may want to look at [How to Contribute to an Open Source
+Project on GitHub][how-contribute]. In brief, we use [GitHub flow][github-flow] to manage
+changes:
 
-> [!TIP]
-> Consider using an IDE (e.g., [VSCode][vscode]) or a GUI client (e.g., [GitHub Desktop][github-desktop]) to help 
-> you with some of the common steps described below.
+> [!TIP] Consider using an IDE (e.g., [VSCode][vscode]) or a GUI client (e.g., [GitHub
+> Desktop][github-desktop]) to help you with some of the common steps described below.
 
-1. Fork the [vuecore][vuecore-repo] repo on GitHub. 
+1. Fork the [vuecore][vuecore-repo] repo on GitHub.
 2. Clone your fork locally. Replace `yourusername` with your GitHub username.
 
    ```bash
    git clone https://github.com/yourusername/vuecore.git
    ```
 
-3. Install your local copy into a virtual environment. Assuming you have Python available 
-   on your system, this can be done using `venv`. Alternatives are `conda`, `uv`, or `poetry` 
-   to create and manage virtual environments.
+3. Install your local copy into a virtual environment. Assuming you have Python available
+   on your system, this can be done using `venv`. Alternatives are `conda`, `uv`, or
+   `poetry` to create and manage virtual environments.
 
    ```bash
    cd vuecore/
@@ -78,15 +82,16 @@ In brief, we use [GitHub flow][github-flow] to manage changes:
    pip install -e .[dev]
    ```
 
-4. Create a new branch in your desktop copy of this repository for each significant change.
+4. Create a new branch in your desktop copy of this repository for each significant
+   change.
 
    ```bash
    git checkout -b name-of-your-new-branch
    ```
 
-5. When you're done making changes, check that your changes are formatted and pass `black` and
-   `ruff` checks (some changes ruff can automatically fix for you, if you pass the `--fix` flag). 
-   Also, run the `tests` to make sure everything is working as expected:
+5. When you're done making changes, check that your changes are formatted and pass `black`
+   and `ruff` checks (some changes ruff can automatically fix for you, if you pass the
+   `--fix` flag). Also, run the `tests` to make sure everything is working as expected:
 
    ```bash
    black .
@@ -107,36 +112,41 @@ In brief, we use [GitHub flow][github-flow] to manage changes:
    git push origin name-of-your-new-branch
    ```
 
-8. Submit a pull request from that branch to the [upstream repository][vuecore-repo] via GitHub.
-   See the **PR General Guidelines** below for more details.
-9. If you receive feedback, make changes on your desktop and push to your branch on GitHub: the 
-   pull request will update automatically.
+8. Submit a pull request from that branch to the [upstream repository][vuecore-repo] via
+   GitHub. See the **PR General Guidelines** below for more details.
+9. If you receive feedback, make changes on your desktop and push to your branch on
+   GitHub: the pull request will update automatically.
 
-> [!TIP]
-> The documentation for [Git][git-docs] and [GitHub][github-docs] are easy to follow, and you can learn the 
-> basics using their official guides.
+> [!TIP] The documentation for [Git][git-docs] and [GitHub][github-docs] are easy to
+> follow, and you can learn the basics using their official guides.
 
 #### PR General Guidelines
 
-We have a general [PR template][general-pr-template] that is loaded autmatically when you open a new PR. 
-Also, if you are adding a new plot, we created a [new plot PR template][new-plot-pr-template]
-with a checklist of all the steps to follow, which you can use with a query paramter by clicking [here][new-plot-pr-query-param].
+We have a general [PR template][general-pr-template] that is loaded autmatically when you
+open a new PR. Also, if you are adding a new plot, we created a [new plot PR
+template][new-plot-pr-template] with a checklist of all the steps to follow, which you can
+use with a query paramter by clicking [here][new-plot-pr-query-param].
 
 Before you submit a PR, check that it meets these guidelines:
 
 1. The pull request should include tests.
-2. If the pull request adds functionality, the docs should be updated. Put
-   your new functionality into a function with a docstring.
+2. If the pull request adds functionality, the docs should be updated. Put your new
+   functionality into a function with a docstring.
 3. The pull request should pass the workflows on GitHub.
 
 ## Code & Documentation Standards
 
-To maintain consistency across the codebase, please adhere to the following standards when contributing:
+To maintain consistency across the codebase, please adhere to the following standards when
+contributing:
 
-* **Docstrings:** Follow the [NumPy docstring style][numpy-docstring-guide]. Include examples where relevant.
-* **Type Hints:** Use Python type hints for function signatures and variable annotations (**PEP 484**).
-* **Code Formatting:** Use `black` for code formatting and `ruff` for linting (as mentioned in the PR guidelines).
-* **Naming Conventions:** Follow **PEP8** for naming (e.g., snake_case for variables/functions, CamelCase for classes).
+- **Docstrings:** Follow the [NumPy docstring style][numpy-docstring-guide]. Include
+  examples where relevant.
+- **Type Hints:** Use Python type hints for function signatures and variable annotations
+  (**PEP 484**).
+- **Code Formatting:** Use `black` for code formatting and `ruff` for linting (as
+  mentioned in the PR guidelines).
+- **Naming Conventions:** Follow **PEP8** for naming (e.g., snake_case for
+  variables/functions, CamelCase for classes).
 
 Here is an example of a simple function with a proper docstring and type hints:
 
@@ -163,19 +173,23 @@ def calculate_average(values: List[float]) -> float:
     return sum(values) / len(values)
 ```
 
-## Test Guidelines 
+## Test Guidelines
 
-We encourage comprehensive testing to maintain code quality, so all contributions should include 
-appropriate tests that verify functionality. We use `pytest` as our testing framework. Here are some considerations:
+We encourage comprehensive testing to maintain code quality, so all contributions should
+include appropriate tests that verify functionality. We use `pytest` as our testing
+framework. Here are some considerations:
 
-* **Structure:** Place tests in the tests/ directory, mirroring the source structure.
-* **Coverage:** Aim for high test coverage, especially for new features or bug fixes. Try to cover typical use cases as well as edge cases.
-* **Naming:** Use descriptive test function names that indicate what is being tested.
-* **Docstrings:** Include docstrings in your test functions to explain their purpose, following the previous docstring guidelines.
-* **Isolation:** Each test should be independent and not rely on other tests.
-* **Local Execution:** Ensure that tests can be run locally using `pytest` before submitting a PR.
+- **Structure:** Place tests in the tests/ directory, mirroring the source structure.
+- **Coverage:** Aim for high test coverage, especially for new features or bug fixes. Try
+  to cover typical use cases as well as edge cases.
+- **Naming:** Use descriptive test function names that indicate what is being tested.
+- **Docstrings:** Include docstrings in your test functions to explain their purpose,
+  following the previous docstring guidelines.
+- **Isolation:** Each test should be independent and not rely on other tests.
+- **Local Execution:** Ensure that tests can be run locally using `pytest` before
+  submitting a PR.
 
-Here is an example of a test script for the `calculate_average` function: 
+Here is an example of a test script for the `calculate_average` function:
 
 ```python
 import pytest
@@ -203,23 +217,26 @@ Run the following command in the root directory to execute the tests locally:
 pytest .
 ```
 
-It's possible to run specific test files or functions by providing their paths. 
-See the [pytest documentation][pytest-docs] for more details.
+It's possible to run specific test files or functions by providing their paths. See the
+[pytest documentation][pytest-docs] for more details.
 
 ## Deployment
 
-We created a [CI/CD worflow][cicd-workflow] using **GitHub Actions** to automatically deploy the Python package to 
-[PyP][vuecore-pypi] when a new release is created. To create a new release, make sure all changed are merged into the `main` branch, 
-then go to the [Releases section][releases-vuecore] of the GitHub repository and click on **Draft a new release**. Fill in the 
-release title and description, then click on **Publish release**. This will trigger the GitHub Actions workflow to build and deploy the package to PyPI.
+We created a [CI/CD worflow][cicd-workflow] using **GitHub Actions** to automatically
+deploy the Python package to [PyP][vuecore-pypi] when a new release is created. To create
+a new release, make sure all changed are merged into the `main` branch, then go to the
+[Releases section][releases-vuecore] of the GitHub repository and click on **Draft a new
+release**. Fill in the release title and description, then click on **Publish release**.
+This will trigger the GitHub Actions workflow to build and deploy the package to PyPI.
 
-Also, we have a GitHub Action that automatically deploys the documentation to [Read the Docs][vuecore-docs] in
-every push to a branch or when a PR is merged into `main`.
+Also, we have a GitHub Action that automatically deploys the documentation to [Read the
+Docs][vuecore-docs] in every push to a branch or when a PR is merged into `main`.
 
 ## Credits
 
-This contribution guide was modified under the [Creative Commons Attribution 4.0 International License][ccby] from 
-the [Software Carpentry guides][soft-cp-guides] and the [acore][acore-repo] project.
+This contribution guide was modified under the [Creative Commons Attribution 4.0
+International License][ccby] from the [Software Carpentry guides][soft-cp-guides] and the
+[acore][acore-repo] project.
 
 [vuecore-repo]: https://github.com/Multiomics-Analytics-Group/vuecore
 [vuecore-docs]: https://vuecore.readthedocs.io/

docs/.gitignore

@@ -5,4 +5,4 @@ _build
 jupyter_execute
 
 # VsCode
-*.DS_Store
+*.DS_Store