cnsplots 0.0.1__tar.gz

cnsplots-0.0.1/LICENSE.md

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2023-2026, Farid Rashidi
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cnsplots-0.0.1/PKG-INFO

@@ -0,0 +1,359 @@
+Metadata-Version: 2.4
+Name: cnsplots
+Version: 0.0.1
+Summary: A comprehensive plotting library for bioinformatics and data visualization
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/faridrashidi/cnsplots
+Project-URL: Documentation, https://cnsplots.readthedocs.io
+Project-URL: Repository, https://github.com/faridrashidi/cnsplots
+Project-URL: Issues, https://github.com/faridrashidi/cnsplots/issues
+Keywords: plotting,visualization,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <4.0,>=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: adjustText
+Requires-Dist: biopython
+Requires-Dist: glasbey
+Requires-Dist: gseapy
+Requires-Dist: lifelines
+Requires-Dist: lxml
+Requires-Dist: matplotlib
+Requires-Dist: matplotlib-venn
+Requires-Dist: natsort
+Requires-Dist: num2tex
+Requires-Dist: numba>=0.58.1
+Requires-Dist: numpy
+Requires-Dist: palettable
+Requires-Dist: pandas
+Requires-Dist: pycomplexheatmap
+Requires-Dist: scanpy
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: statannotations
+Requires-Dist: statsmodels
+Requires-Dist: upsetplot
+Provides-Extra: dev
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: fastcluster; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Provides-Extra: doc
+Requires-Dist: furo; extra == "doc"
+Requires-Dist: myst-parser; extra == "doc"
+Requires-Dist: sphinx<9; python_version < "3.11" and extra == "doc"
+Requires-Dist: sphinx<9.1,>=9; python_version >= "3.11" and extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinx-gallery; extra == "doc"
+Dynamic: license-file
+
+# cnsplots
+
+<div align="center">
+
+[![PyPI](https://img.shields.io/pypi/v/cnsplots?logo=pypi&logoColor=white&style=flat-square)](https://pypi.org/project/cnsplots/)
+[![Python Version](https://img.shields.io/pypi/pyversions/cnsplots?logo=python&logoColor=white&style=flat-square)](https://pypi.org/project/cnsplots/)
+[![License](https://img.shields.io/pypi/l/cnsplots.svg?logo=creativecommons&logoColor=white&style=flat-square&color=blueviolet)](https://github.com/faridrashidi/cnsplots/blob/main/LICENSE.md)
+[![Code Style](https://img.shields.io/badge/code%20style-ruff-000000.svg?logo=ruff&logoColor=white&style=flat-square)](https://github.com/astral-sh/ruff)
+
+**Publication-Ready Scientific Plots for Cell, Nature, and Science Journals**
+
+Create visually stunning, journal-quality figures with minimal code. Built on matplotlib, fully compatible with seaborn, and optimized for Adobe Illustrator.
+
+[Documentation](https://cnsplots.farid.one/) · [Examples Gallery](https://cnsplots.farid.one/examples/index.html) · [Report Bug](https://github.com/faridrashidi/cnsplots/issues) · [Request Feature](https://github.com/faridrashidi/cnsplots/issues)
+
+</div>
+
+---
+
+## Overview
+
+[![Overview](docs/_static/images/overview.png?raw=true)](https://cnsplots.farid.one/examples/index.html)
+
+**cnsplots** is a Python visualization library designed specifically for creating publication-ready scientific figures. It takes care of the tedious styling details so you can focus on your science.
+
+### Why cnsplots?
+
+- 🎨 **Publication-Ready**: Pre-configured styles matching Cell, Nature, and Science journal requirements
+- 🎯 **Simple API**: Create complex multi-panel figures with just a few lines of code
+- 📐 **Precise Control**: Specify dimensions in pixels, perfect for journal submission guidelines
+- 🖋️ **Adobe Illustrator Compatible**: SVG exports with editable fonts (no text-to-path conversion)
+- 📊 **Statistical Integration**: Built-in statistical tests and annotations
+- 🔧 **Highly Customizable**: Full control over colors, fonts, and styling
+- 🌈 **Rich Color Palettes**: Curated color schemes optimized for scientific visualization
+- 🧩 **Multi-Panel Support**: Easy creation of complex figure layouts
+
+## Features
+
+### 📊 25+ Plot Types
+
+**Basic Plots**
+
+- Box plots, violin plots, bar plots, strip plots
+- Scatter plots, line plots, regression plots
+- Histograms, KDE plots, ridge plots
+
+**Scientific Plots**
+
+- Survival plots (Kaplan-Meier)
+- Cumulative incidence plots
+- ROC curves and forest plots
+- Volcano plots and GSEA plots
+- Confusion matrices
+
+**Specialized Plots**
+
+- Heatmaps with hierarchical clustering
+- Dot plots for enrichment
+- Venn diagrams and UpSet plots
+- Sankey diagrams
+- Pie and donut charts
+- QQ plots and slope plots
+
+### 🎨 Beautiful Color Palettes
+
+Multiple curated palettes including:
+
+- **Qualitative**: Ecotyper1-6, Set1-3, Tableau, Bold
+- **Sequential**: Parula, gnuplot, custom gradients
+- **Diverging**: BlueRed, BuRd_custom, OrBu_custom
+
+### 📐 Multi-Panel Figures
+
+Create complex layouts with automatic panel labeling (A, B, C...):
+
+```python
+import cnsplots as cns
+
+mp = cns.multipanel(max_width=540)
+
+# Panel A
+mp.panel("A", height=150, width=150)
+cns.boxplot(data=df1, x="group", y="value")
+
+# Panel B
+mp.panel("B", height=150, width=150)
+cns.scatterplot(data=df2, x="x", y="y")
+
+# Continues...
+```
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install cnsplots
+```
+
+### For Development
+
+First install [uv](https://docs.astral.sh/uv/), then:
+
+```bash
+git clone https://github.com/faridrashidi/cnsplots
+cd cnsplots
+make install
+```
+
+## Quick Start
+
+### Basic Usage
+
+```python
+import cnsplots as cns
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+# Load example data
+df = sns.load_dataset("tips")
+
+# Create a figure (dimensions in pixels)
+cns.figure(height=150, width=100)
+
+# Create a publication-ready boxplot
+cns.boxplot(data=df, x="day", y="total_bill")
+
+# Save as vector graphic
+plt.savefig("figure.svg")
+```
+
+### Statistical Comparisons
+
+```python
+# Add statistical significance annotations
+cns.figure(150, 150)
+cns.boxplot(
+    data=df,
+    x="day",
+    y="total_bill",
+    pairs=[("Thur", "Fri"), ("Sat", "Sun")],  # Compare these pairs
+)
+# Prints: P-values were determined by two-sided Mann-Whitney U test.
+```
+
+### Custom Colors
+
+```python
+# Use custom color palette
+cns.figure(150, 200, color_cycle="Ecotyper1")
+cns.violinplot(data=df, x="day", y="total_bill", hue="sex")
+```
+
+## Examples Gallery
+
+Explore our comprehensive [examples gallery](https://cnsplots.farid.one/examples/index.html) featuring:
+
+- 📦 Basic statistical plots
+- 🧬 Genomics and bioinformatics visualizations
+- 📈 Time-series and survival analysis
+- 🎯 Machine learning results (ROC, confusion matrices)
+- 🔬 Multi-omics data visualization
+- 🎨 Custom color schemes and styling
+
+## Documentation
+
+Full documentation is available at [farid.one/cnsplots](https://cnsplots.farid.one/)
+
+- [Installation Guide](https://cnsplots.farid.one/installation.html)
+- [API Reference](https://cnsplots.farid.one/api.html)
+- [Examples Gallery](https://cnsplots.farid.one/examples/index.html)
+
+## Key Concepts
+
+### Figure Dimensions
+
+Specify sizes in **pixels** for precise control:
+
+```python
+cns.figure(height=150, width=100)  # Creates 150px × 100px figure
+```
+
+### Color Palettes
+
+Access curated color palettes:
+
+```python
+# Qualitative palettes (for categorical data)
+cns.figure(color_cycle="Ecotyper1")  # Default, optimized for journals
+cns.figure(color_cycle="Set1")  # ColorBrewer Set1
+
+# Sequential palettes (for continuous data)
+cns.figure(color_map="parula")  # MATLAB-style
+cns.figure(color_map="gnuplot")  # Default sequential
+
+# Get individual colors
+red = cns.RED
+blue = cns.BLUE
+```
+
+### Statistical Tests
+
+Many plot functions include built-in statistical testing:
+
+```python
+# Boxplot with Mann-Whitney U test
+cns.boxplot(data=df, x="group", y="value", pairs="all")
+
+# Barplot with Welch's t-test
+cns.barplot(data=df, x="group", y="value", pairs=[("A", "B")])
+
+# Stackplot with Fisher's exact test
+cns.stackplot(data=df, x="group", y="category", pairs=[("A", "B")])
+```
+
+### Export for Publication
+
+```python
+# SVG for vector graphics (recommended)
+plt.savefig("figure.svg")
+
+# High-resolution PNG
+plt.savefig("figure.png", dpi=300)
+
+# PDF with editable text
+plt.savefig("figure.pdf")
+```
+
+## Requirements
+
+- Python ≥ 3.9
+- Core: matplotlib, numpy, pandas, seaborn
+- Optional: lifelines, gseapy, scanpy (for specific plot types)
+
+See [pyproject.toml](pyproject.toml) for complete dependency list.
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
+
+### Development Setup
+
+Follow the development installation instructions above, then use `make lint` to run formatters and linters before submitting a PR.
+
+## Citation
+
+If you use cnsplots in your research, please cite:
+
+```bibtex
+@software{cnsplots,
+  author = {Rashidi, Farid},
+  title = {cnsplots: Publication-Ready Scientific Plots},
+  year = {2026},
+  url = {https://github.com/faridrashidi/cnsplots}
+}
+```
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details.
+
+## Acknowledgments
+
+Built with:
+
+- [matplotlib](https://matplotlib.org/) - Core plotting library
+- [seaborn](https://seaborn.pydata.org/) - Statistical visualizations
+- [lifelines](https://lifelines.readthedocs.io/) - Survival analysis
+- [PyComplexHeatmap](https://github.com/DingWB/PyComplexHeatmap) - Complex heatmaps
+- [UpSetPlot](https://upsetplot.readthedocs.io/) - Set intersections
+
+Inspired by the visualization standards of Cell, Nature, and Science journals.
+
+## Support
+
+- 📖 [Documentation](https://cnsplots.farid.one/)
+- 🐛 [Issue Tracker](https://github.com/faridrashidi/cnsplots/issues)
+- 💬 [Discussions](https://github.com/faridrashidi/cnsplots/discussions)
+
+## Related Projects
+
+- [matplotlib](https://matplotlib.org/) - The foundation of Python plotting
+- [seaborn](https://seaborn.pydata.org/) - Statistical data visualization
+- [plotnine](https://plotnine.readthedocs.io/) - Grammar of graphics for Python
+- [altair](https://altair-viz.github.io/) - Declarative visualization
+
+---
+
+<div align="center">
+
+Made with ❤️ for the scientific community
+
+[⭐ Star us on GitHub](https://github.com/faridrashidi/cnsplots) · [📖 Read the Docs](https://cnsplots.farid.one/)
+
+</div>

cnsplots-0.0.1/README.md

@@ -0,0 +1,295 @@
+# cnsplots
+
+<div align="center">
+
+[![PyPI](https://img.shields.io/pypi/v/cnsplots?logo=pypi&logoColor=white&style=flat-square)](https://pypi.org/project/cnsplots/)
+[![Python Version](https://img.shields.io/pypi/pyversions/cnsplots?logo=python&logoColor=white&style=flat-square)](https://pypi.org/project/cnsplots/)
+[![License](https://img.shields.io/pypi/l/cnsplots.svg?logo=creativecommons&logoColor=white&style=flat-square&color=blueviolet)](https://github.com/faridrashidi/cnsplots/blob/main/LICENSE.md)
+[![Code Style](https://img.shields.io/badge/code%20style-ruff-000000.svg?logo=ruff&logoColor=white&style=flat-square)](https://github.com/astral-sh/ruff)
+
+**Publication-Ready Scientific Plots for Cell, Nature, and Science Journals**
+
+Create visually stunning, journal-quality figures with minimal code. Built on matplotlib, fully compatible with seaborn, and optimized for Adobe Illustrator.
+
+[Documentation](https://cnsplots.farid.one/) · [Examples Gallery](https://cnsplots.farid.one/examples/index.html) · [Report Bug](https://github.com/faridrashidi/cnsplots/issues) · [Request Feature](https://github.com/faridrashidi/cnsplots/issues)
+
+</div>
+
+---
+
+## Overview
+
+[![Overview](docs/_static/images/overview.png?raw=true)](https://cnsplots.farid.one/examples/index.html)
+
+**cnsplots** is a Python visualization library designed specifically for creating publication-ready scientific figures. It takes care of the tedious styling details so you can focus on your science.
+
+### Why cnsplots?
+
+- 🎨 **Publication-Ready**: Pre-configured styles matching Cell, Nature, and Science journal requirements
+- 🎯 **Simple API**: Create complex multi-panel figures with just a few lines of code
+- 📐 **Precise Control**: Specify dimensions in pixels, perfect for journal submission guidelines
+- 🖋️ **Adobe Illustrator Compatible**: SVG exports with editable fonts (no text-to-path conversion)
+- 📊 **Statistical Integration**: Built-in statistical tests and annotations
+- 🔧 **Highly Customizable**: Full control over colors, fonts, and styling
+- 🌈 **Rich Color Palettes**: Curated color schemes optimized for scientific visualization
+- 🧩 **Multi-Panel Support**: Easy creation of complex figure layouts
+
+## Features
+
+### 📊 25+ Plot Types
+
+**Basic Plots**
+
+- Box plots, violin plots, bar plots, strip plots
+- Scatter plots, line plots, regression plots
+- Histograms, KDE plots, ridge plots
+
+**Scientific Plots**
+
+- Survival plots (Kaplan-Meier)
+- Cumulative incidence plots
+- ROC curves and forest plots
+- Volcano plots and GSEA plots
+- Confusion matrices
+
+**Specialized Plots**
+
+- Heatmaps with hierarchical clustering
+- Dot plots for enrichment
+- Venn diagrams and UpSet plots
+- Sankey diagrams
+- Pie and donut charts
+- QQ plots and slope plots
+
+### 🎨 Beautiful Color Palettes
+
+Multiple curated palettes including:
+
+- **Qualitative**: Ecotyper1-6, Set1-3, Tableau, Bold
+- **Sequential**: Parula, gnuplot, custom gradients
+- **Diverging**: BlueRed, BuRd_custom, OrBu_custom
+
+### 📐 Multi-Panel Figures
+
+Create complex layouts with automatic panel labeling (A, B, C...):
+
+```python
+import cnsplots as cns
+
+mp = cns.multipanel(max_width=540)
+
+# Panel A
+mp.panel("A", height=150, width=150)
+cns.boxplot(data=df1, x="group", y="value")
+
+# Panel B
+mp.panel("B", height=150, width=150)
+cns.scatterplot(data=df2, x="x", y="y")
+
+# Continues...
+```
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install cnsplots
+```
+
+### For Development
+
+First install [uv](https://docs.astral.sh/uv/), then:
+
+```bash
+git clone https://github.com/faridrashidi/cnsplots
+cd cnsplots
+make install
+```
+
+## Quick Start
+
+### Basic Usage
+
+```python
+import cnsplots as cns
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+# Load example data
+df = sns.load_dataset("tips")
+
+# Create a figure (dimensions in pixels)
+cns.figure(height=150, width=100)
+
+# Create a publication-ready boxplot
+cns.boxplot(data=df, x="day", y="total_bill")
+
+# Save as vector graphic
+plt.savefig("figure.svg")
+```
+
+### Statistical Comparisons
+
+```python
+# Add statistical significance annotations
+cns.figure(150, 150)
+cns.boxplot(
+    data=df,
+    x="day",
+    y="total_bill",
+    pairs=[("Thur", "Fri"), ("Sat", "Sun")],  # Compare these pairs
+)
+# Prints: P-values were determined by two-sided Mann-Whitney U test.
+```
+
+### Custom Colors
+
+```python
+# Use custom color palette
+cns.figure(150, 200, color_cycle="Ecotyper1")
+cns.violinplot(data=df, x="day", y="total_bill", hue="sex")
+```
+
+## Examples Gallery
+
+Explore our comprehensive [examples gallery](https://cnsplots.farid.one/examples/index.html) featuring:
+
+- 📦 Basic statistical plots
+- 🧬 Genomics and bioinformatics visualizations
+- 📈 Time-series and survival analysis
+- 🎯 Machine learning results (ROC, confusion matrices)
+- 🔬 Multi-omics data visualization
+- 🎨 Custom color schemes and styling
+
+## Documentation
+
+Full documentation is available at [farid.one/cnsplots](https://cnsplots.farid.one/)
+
+- [Installation Guide](https://cnsplots.farid.one/installation.html)
+- [API Reference](https://cnsplots.farid.one/api.html)
+- [Examples Gallery](https://cnsplots.farid.one/examples/index.html)
+
+## Key Concepts
+
+### Figure Dimensions
+
+Specify sizes in **pixels** for precise control:
+
+```python
+cns.figure(height=150, width=100)  # Creates 150px × 100px figure
+```
+
+### Color Palettes
+
+Access curated color palettes:
+
+```python
+# Qualitative palettes (for categorical data)
+cns.figure(color_cycle="Ecotyper1")  # Default, optimized for journals
+cns.figure(color_cycle="Set1")  # ColorBrewer Set1
+
+# Sequential palettes (for continuous data)
+cns.figure(color_map="parula")  # MATLAB-style
+cns.figure(color_map="gnuplot")  # Default sequential
+
+# Get individual colors
+red = cns.RED
+blue = cns.BLUE
+```
+
+### Statistical Tests
+
+Many plot functions include built-in statistical testing:
+
+```python
+# Boxplot with Mann-Whitney U test
+cns.boxplot(data=df, x="group", y="value", pairs="all")
+
+# Barplot with Welch's t-test
+cns.barplot(data=df, x="group", y="value", pairs=[("A", "B")])
+
+# Stackplot with Fisher's exact test
+cns.stackplot(data=df, x="group", y="category", pairs=[("A", "B")])
+```
+
+### Export for Publication
+
+```python
+# SVG for vector graphics (recommended)
+plt.savefig("figure.svg")
+
+# High-resolution PNG
+plt.savefig("figure.png", dpi=300)
+
+# PDF with editable text
+plt.savefig("figure.pdf")
+```
+
+## Requirements
+
+- Python ≥ 3.9
+- Core: matplotlib, numpy, pandas, seaborn
+- Optional: lifelines, gseapy, scanpy (for specific plot types)
+
+See [pyproject.toml](pyproject.toml) for complete dependency list.
+
+## Contributing
+
+Contributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.
+
+### Development Setup
+
+Follow the development installation instructions above, then use `make lint` to run formatters and linters before submitting a PR.
+
+## Citation
+
+If you use cnsplots in your research, please cite:
+
+```bibtex
+@software{cnsplots,
+  author = {Rashidi, Farid},
+  title = {cnsplots: Publication-Ready Scientific Plots},
+  year = {2026},
+  url = {https://github.com/faridrashidi/cnsplots}
+}
+```
+
+## License
+
+This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details.
+
+## Acknowledgments
+
+Built with:
+
+- [matplotlib](https://matplotlib.org/) - Core plotting library
+- [seaborn](https://seaborn.pydata.org/) - Statistical visualizations
+- [lifelines](https://lifelines.readthedocs.io/) - Survival analysis
+- [PyComplexHeatmap](https://github.com/DingWB/PyComplexHeatmap) - Complex heatmaps
+- [UpSetPlot](https://upsetplot.readthedocs.io/) - Set intersections
+
+Inspired by the visualization standards of Cell, Nature, and Science journals.
+
+## Support
+
+- 📖 [Documentation](https://cnsplots.farid.one/)
+- 🐛 [Issue Tracker](https://github.com/faridrashidi/cnsplots/issues)
+- 💬 [Discussions](https://github.com/faridrashidi/cnsplots/discussions)
+
+## Related Projects
+
+- [matplotlib](https://matplotlib.org/) - The foundation of Python plotting
+- [seaborn](https://seaborn.pydata.org/) - Statistical data visualization
+- [plotnine](https://plotnine.readthedocs.io/) - Grammar of graphics for Python
+- [altair](https://altair-viz.github.io/) - Declarative visualization
+
+---
+
+<div align="center">
+
+Made with ❤️ for the scientific community
+
+[⭐ Star us on GitHub](https://github.com/faridrashidi/cnsplots) · [📖 Read the Docs](https://cnsplots.farid.one/)
+
+</div>