# RNApysoforms <img src="./assets/RNA-pysoforms-logo.png" align="right" height="80" />
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`RNApysoforms` is a Python package designed for visualizing RNA isoform structures and expression levels. Leveraging Plotly for interactive plotting and Polars for efficient data manipulation, it enables the creation of fast-rendering, interactive plots suitable for both local and web applications. Inspired by the R package [ggtranscript](https://github.com/dzhang32/ggtranscript), RNApysoforms brings similar RNA visualization capabilities to the Python ecosystem, facilitating effective exploration and presentation of RNA sequencing data.
## Pre-print for citation
https://www.biorxiv.org/content/10.1101/2024.11.06.622357v1
## Important
### RNApysoforms expects feature start and end coordinates in GTF format, where coordinates are 1-indexed and inclusive on both ends.
## Installation
You can install `RNApysoforms` using pip:
```bash
pip install RNApysoforms
```
## Quick Start
[Basic usage (quick start)](https://rna-pysoforms.readthedocs.io/en/latest/examples/basic_usage.html)
## More vignettes (usage examples)
[Rescaling introns for a prettier RNA isoform structure plot](https://rna-pysoforms.readthedocs.io/en/latest/examples/rescaled_introns.html)
[Plotting RNA isoform structure and expression](https://rna-pysoforms.readthedocs.io/en/latest/examples/expression_plot.html)
[Plotting RNA isoform structure and normalized expression](https://rna-pysoforms.readthedocs.io/en/latest/examples/expression_plot_filtered_and_ordered.html)
## Test data and documentation
[Download small test dataset](https://zenodo.org/records/13961009/files/RNApysoforms_test_data.zip?download=1)
[Function documentation and vignettes](https://rna-pysoforms.readthedocs.io/en/latest/index.html)
## Issues
Please go through the [documentation and vignettes](https://rna-pysoforms.readthedocs.io/en/latest/index.html) before submitting an issue.
## Contributing
Contributions to `RNApysoforms` are welcome! Please feel free to submit a Pull Request.
The function implementations are under the `src/RNApysoforms` directory.
## Functions
- [calculate_exon_number()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.calculate_exon_number.html): Assigns exon numbers to exons, CDS, and introns within a genomic annotation dataset based on transcript structure and strand direction.
- [gene_filtering()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.gene_filtering.html): Filters genomic annotations and optionally an expression matrix for a specific gene, with options to order and select top expressed transcripts.
- [make_plot()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.make_plot.html): Creates a Plotly figure panel for transcript structure plots and/or expression data plots.
- [make_traces()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.make_traces.html): Generates Plotly traces for visualizing transcript structures and expression data.
- [read_expression_matrix()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.read_expression_matrix.html): Loads and processes an expression matrix, optionally merging with metadata, performing CPM normalization, and calculating relative transcript abundance.
- [read_ensembl_gtf()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.read_ensembl_gtf.html): Reads an ENSEMBL GTF (Gene Transfer Format) file and returns the data as a Polars DataFrame.
- [shorten_gaps()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.shorten_gaps.html): Shortens intron and transcript start gaps between exons in genomic annotations to enhance visualization.
- [to_intron()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.to_intron.html): Converts exon coordinates into corresponding intron coordinates within a genomic annotation dataset.
## License
This project is licensed under the MIT License.
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"description": "# RNApysoforms <img src=\"./assets/RNA-pysoforms-logo.png\" align=\"right\" height=\"80\" />\r\n\r\n\r\n<!-- badges: start -->\r\n[](https://github.com/UK-SBCoA-EbbertLab/RNApysoforms/actions/workflows/main.yml)\r\n[](https://app.codecov.io/gh/UK-SBCoA-EbbertLab/RNApysoforms?branch=main)\r\n[](https://lifecycle.r-lib.org/articles/stages.html#stable)\r\n[](https://github.com/UK-SBCoA-EbbertLab/RNApysoforms/issues)\r\n[](https://github.com/UK-SBCoA-EbbertLab/RNApysoforms/pulls)\r\n[](https://rna-pysoforms.readthedocs.io/en/latest/?badge=latest)\r\n[](https://doi.org/10.5281/zenodo.14052788)\r\n\r\n<!-- badges: end -->\r\n\r\n\r\n`RNApysoforms` is a Python package designed for visualizing RNA isoform structures and expression levels. Leveraging Plotly for interactive plotting and Polars for efficient data manipulation, it enables the creation of fast-rendering, interactive plots suitable for both local and web applications. Inspired by the R package [ggtranscript](https://github.com/dzhang32/ggtranscript), RNApysoforms brings similar RNA visualization capabilities to the Python ecosystem, facilitating effective exploration and presentation of RNA sequencing data.\r\n\r\n## Pre-print for citation\r\n\r\nhttps://www.biorxiv.org/content/10.1101/2024.11.06.622357v1\r\n\r\n\r\n## Important\r\n\r\n### RNApysoforms expects feature start and end coordinates in GTF format, where coordinates are 1-indexed and inclusive on both ends.\r\n\r\n\r\n## Installation\r\n\r\nYou can install `RNApysoforms` using pip:\r\n\r\n```bash\r\npip install RNApysoforms\r\n```\r\n\r\n\r\n## Quick Start\r\n\r\n[Basic usage (quick start)](https://rna-pysoforms.readthedocs.io/en/latest/examples/basic_usage.html)\r\n\r\n\r\n## More vignettes (usage examples)\r\n\r\n[Rescaling introns for a prettier RNA isoform structure plot](https://rna-pysoforms.readthedocs.io/en/latest/examples/rescaled_introns.html)\r\n\r\n[Plotting RNA isoform structure and expression](https://rna-pysoforms.readthedocs.io/en/latest/examples/expression_plot.html)\r\n\r\n[Plotting RNA isoform structure and normalized expression](https://rna-pysoforms.readthedocs.io/en/latest/examples/expression_plot_filtered_and_ordered.html)\r\n\r\n\r\n\r\n## Test data and documentation\r\n\r\n[Download small test dataset](https://zenodo.org/records/13961009/files/RNApysoforms_test_data.zip?download=1)\r\n\r\n[Function documentation and vignettes](https://rna-pysoforms.readthedocs.io/en/latest/index.html)\r\n\r\n\r\n## Issues\r\n\r\nPlease go through the [documentation and vignettes](https://rna-pysoforms.readthedocs.io/en/latest/index.html) before submitting an issue.\r\n\r\n\r\n## Contributing\r\n\r\nContributions to `RNApysoforms` are welcome! Please feel free to submit a Pull Request.\r\n\r\nThe function implementations are under the `src/RNApysoforms` directory.\r\n\r\n\r\n## Functions\r\n\r\n- [calculate_exon_number()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.calculate_exon_number.html): Assigns exon numbers to exons, CDS, and introns within a genomic annotation dataset based on transcript structure and strand direction.\r\n\r\n- [gene_filtering()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.gene_filtering.html): Filters genomic annotations and optionally an expression matrix for a specific gene, with options to order and select top expressed transcripts.\r\n\r\n- [make_plot()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.make_plot.html): Creates a Plotly figure panel for transcript structure plots and/or expression data plots.\r\n\r\n- [make_traces()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.make_traces.html): Generates Plotly traces for visualizing transcript structures and expression data.\r\n\r\n- [read_expression_matrix()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.read_expression_matrix.html): Loads and processes an expression matrix, optionally merging with metadata, performing CPM normalization, and calculating relative transcript abundance.\r\n\r\n- [read_ensembl_gtf()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.read_ensembl_gtf.html): Reads an ENSEMBL GTF (Gene Transfer Format) file and returns the data as a Polars DataFrame.\r\n\r\n- [shorten_gaps()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.shorten_gaps.html): Shortens intron and transcript start gaps between exons in genomic annotations to enhance visualization.\r\n\r\n- [to_intron()](https://rna-pysoforms.readthedocs.io/en/latest/_autosummary/RNApysoforms.to_intron.html): Converts exon coordinates into corresponding intron coordinates within a genomic annotation dataset.\r\n\r\n\r\n## License\r\n\r\nThis project is licensed under the MIT License.\r\n",
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