pylocuszoom 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (12) hide show
  1. pylocuszoom/backends/base.py +2 -0
  2. pylocuszoom/backends/bokeh_backend.py +220 -48
  3. pylocuszoom/backends/matplotlib_backend.py +29 -7
  4. pylocuszoom/backends/plotly_backend.py +262 -20
  5. pylocuszoom/finemapping.py +0 -1
  6. pylocuszoom/gene_track.py +231 -23
  7. pylocuszoom/plotter.py +277 -139
  8. {pylocuszoom-0.2.0.dist-info → pylocuszoom-0.3.0.dist-info}/METADATA +28 -14
  9. pylocuszoom-0.3.0.dist-info/RECORD +21 -0
  10. pylocuszoom-0.2.0.dist-info/RECORD +0 -21
  11. {pylocuszoom-0.2.0.dist-info → pylocuszoom-0.3.0.dist-info}/WHEEL +0 -0
  12. {pylocuszoom-0.2.0.dist-info → pylocuszoom-0.3.0.dist-info}/licenses/LICENSE.md +0 -0
{pylocuszoom-0.2.0.dist-info → pylocuszoom-0.3.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: pylocuszoom
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- Version: 0.2.0
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+ Version: 0.3.0
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  Summary: Regional association plots for GWAS results with LD coloring, gene tracks, and recombination rate overlays
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  Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
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  Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
@@ -19,6 +19,7 @@ Classifier: Programming Language :: Python :: 3.12
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  Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Classifier: Topic :: Scientific/Engineering :: Visualization
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  Requires-Python: >=3.10
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+ Requires-Dist: adjusttext>=0.8
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  Requires-Dist: bokeh>=3.8.2
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  Requires-Dist: kaleido>=0.2.0
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  Requires-Dist: loguru>=0.7.0
@@ -28,14 +29,11 @@ Requires-Dist: pandas>=1.4.0
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  Requires-Dist: plotly>=5.0.0
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  Requires-Dist: pyliftover>=0.4
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  Provides-Extra: all
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- Requires-Dist: adjusttext>=0.8; extra == 'all'
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  Requires-Dist: pyspark>=3.0.0; extra == 'all'
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  Provides-Extra: dev
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  Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
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  Requires-Dist: pytest>=7.0.0; extra == 'dev'
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  Requires-Dist: ruff>=0.1.0; extra == 'dev'
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- Provides-Extra: labels
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- Requires-Dist: adjusttext>=0.8; extra == 'labels'
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  Provides-Extra: spark
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  Requires-Dist: pyspark>=3.0.0; extra == 'spark'
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  Description-Content-Type: text/markdown
@@ -75,14 +73,20 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
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  ## Installation
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+ ```bash
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+ pip install pylocuszoom
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+ ```
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+
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+ Or with uv:
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+
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  ```bash
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  uv add pylocuszoom
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  ```
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- Or with pip:
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+ Or with conda (Bioconda):
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  ```bash
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- pip install pylocuszoom
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+ conda install -c bioconda pylocuszoom
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  ```
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  ## Quick Start
@@ -165,20 +169,30 @@ fig = plotter.plot(
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  )
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  ```
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- ## Interactive Backends (Coming Soon)
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+ ## Backends
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- > **Note:** Interactive backends (plotly, bokeh) are planned but not yet fully integrated. Currently all plots use matplotlib.
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+ pyLocusZoom supports multiple rendering backends:
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  ```python
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- # Static publication-quality plot (default, currently only supported backend)
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- plotter = LocusZoomPlotter(species="canine", backend="matplotlib")
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- fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
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+ # Static publication-quality plot (default)
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+ fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="matplotlib")
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  fig.savefig("plot.png", dpi=150)
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+
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+ # Interactive Plotly (hover tooltips, pan/zoom)
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+ fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="plotly")
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+ fig.write_html("plot.html")
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+
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+ # Interactive Bokeh (dashboard-ready)
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+ fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh")
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  ```
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- Future releases will support:
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- - **Plotly**: Interactive plots with hover tooltips, zoom/pan
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- - **Bokeh**: Dashboard-friendly interactive plots
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+ | Backend | Output | Best For |
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+ |---------|--------|----------|
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+ | `matplotlib` | Static PNG/PDF/SVG | Publications, presentations |
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+ | `plotly` | Interactive HTML | Web reports, data exploration |
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+ | `bokeh` | Interactive HTML | Dashboards, web apps |
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+
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+ > **Note:** All backends support gene track, recombination overlay, and LD legend. SNP labels (auto-positioned with adjustText) are matplotlib-only.
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  ## Stacked Plots
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pylocuszoom-0.3.0.dist-info/RECORD ADDED
@@ -0,0 +1,21 @@
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+ pylocuszoom/__init__.py,sha256=f8h22YYL3JkDP5P_dJftu98qlJkXvaAeyto5kVc8bzU,3785
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+ pylocuszoom/colors.py,sha256=XXTCmCFfHrOrSiP6b0V8Kis7Z1tyvGEKJpdv59QDVQ8,6610
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+ pylocuszoom/eqtl.py,sha256=9lZJ8jT1WEj3won6D9B54xdqUvbRvxpOitf97NCUR28,6167
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+ pylocuszoom/finemapping.py,sha256=PJ4HJYeCaHZecUmADCEGQxKd9HhhjrdIA1H5LQsUmLI,6332
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+ pylocuszoom/gene_track.py,sha256=CbKqIIl-3VpqIS0NWQ7p-VazhrgbF0-XDkkvoWx_2jI,18665
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+ pylocuszoom/labels.py,sha256=Ams5WVZFNVT692BRiQ5wZcdbdNEAm5xtgRwmF5u0s_A,3492
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+ pylocuszoom/ld.py,sha256=64xIulpDVvbMSryWUPoCQ99Odcjwf1wejpwVr_30MLU,6412
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+ pylocuszoom/logging.py,sha256=nZHEkbnjp8zoyWj_S-Hy9UQvUYLoMoxyiOWRozBT2dg,4987
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+ pylocuszoom/plotter.py,sha256=7wEN0b3emb0SM7gYn8bSjXBGNt7npw3y3y5AEC-Ha2k,43660
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+ pylocuszoom/recombination.py,sha256=Q2tAft54nJWHlZt-vZje1r_5RP7D8_VUy5ab_deYXVw,13749
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+ pylocuszoom/utils.py,sha256=fKNX9WSTbfHR1EpPYijt6ycNjXEjwzunQMHXAvHaK3s,5211
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+ pylocuszoom/backends/__init__.py,sha256=7dlGvDoqMVK3fCtoMcI9zOP9qO0odQGPwfXhxnLfXfI,1196
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+ pylocuszoom/backends/base.py,sha256=YEYMtaqPRTJQI-TPqK62-XPN6WvjVwqP6e6ydULK6H0,8523
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+ pylocuszoom/backends/bokeh_backend.py,sha256=oOXTOhSx-tNgBzgtYfYvGUgNmuUP2vhCbtEBOZ5YZ18,18496
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+ pylocuszoom/backends/matplotlib_backend.py,sha256=TIKaT7x0X3QKYUB5076XlG6RC0zbi0hcm3LSU7LGnmw,8521
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+ pylocuszoom/backends/plotly_backend.py,sha256=ucQLmcz6WAdEvII5n3_rdHffZv5-a8FOp8nBGBng-hk,22222
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+ pylocuszoom/reference_data/__init__.py,sha256=qqHqAUt1jebGlCN3CjqW3Z-_coHVNo5K3a3bb9o83hA,109
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+ pylocuszoom-0.3.0.dist-info/METADATA,sha256=P-JbXF9KxFzixMAYKQalKO4F4TwOqxDZD0B0uciyy_c,12068
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+ pylocuszoom-0.3.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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+ pylocuszoom-0.3.0.dist-info/licenses/LICENSE.md,sha256=U2y_hv8RcN5lECA3uK88irU3ODUE1TDAPictcmnP0Q4,698
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+ pylocuszoom-0.3.0.dist-info/RECORD,,
pylocuszoom-0.2.0.dist-info/RECORD DELETED
@@ -1,21 +0,0 @@
1
- pylocuszoom/__init__.py,sha256=f8h22YYL3JkDP5P_dJftu98qlJkXvaAeyto5kVc8bzU,3785
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- pylocuszoom/colors.py,sha256=XXTCmCFfHrOrSiP6b0V8Kis7Z1tyvGEKJpdv59QDVQ8,6610
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- pylocuszoom/eqtl.py,sha256=9lZJ8jT1WEj3won6D9B54xdqUvbRvxpOitf97NCUR28,6167
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- pylocuszoom/finemapping.py,sha256=IZEEF13m8xD2qfnTsqcv67BtPAvqC_FrXdGv1VG8BHk,6351
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- pylocuszoom/gene_track.py,sha256=ZYAWOUHOo9oieovl7VHGCB3j_HBbnr5wwtIwxozgRhE,10854
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- pylocuszoom/labels.py,sha256=Ams5WVZFNVT692BRiQ5wZcdbdNEAm5xtgRwmF5u0s_A,3492
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- pylocuszoom/ld.py,sha256=64xIulpDVvbMSryWUPoCQ99Odcjwf1wejpwVr_30MLU,6412
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- pylocuszoom/logging.py,sha256=nZHEkbnjp8zoyWj_S-Hy9UQvUYLoMoxyiOWRozBT2dg,4987
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- pylocuszoom/plotter.py,sha256=sPqK74B9-ldcKhrrWixyapIdQ4dVgFRERZfJw4ZNS5Y,37865
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- pylocuszoom/recombination.py,sha256=Q2tAft54nJWHlZt-vZje1r_5RP7D8_VUy5ab_deYXVw,13749
11
- pylocuszoom/utils.py,sha256=fKNX9WSTbfHR1EpPYijt6ycNjXEjwzunQMHXAvHaK3s,5211
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- pylocuszoom/backends/__init__.py,sha256=7dlGvDoqMVK3fCtoMcI9zOP9qO0odQGPwfXhxnLfXfI,1196
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- pylocuszoom/backends/base.py,sha256=4EGT4_88y2jvhWm1zAal9v9yuaHhCLo7-rchcWmIK8c,8451
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- pylocuszoom/backends/bokeh_backend.py,sha256=V0yQi1lY96hjTjBXGJtLKGy1LFNii58kTAJiqu0LYPg,12900
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- pylocuszoom/backends/matplotlib_backend.py,sha256=yTTm9KG7e0ct-mvHk_tfJX6SOL97pABsJzs4Xn6H1zw,8010
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- pylocuszoom/backends/plotly_backend.py,sha256=2EDJZczqjZ5gItd3Fb4UaRYGj7SQy7Wgg5UIL8LJ9LM,14128
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- pylocuszoom/reference_data/__init__.py,sha256=qqHqAUt1jebGlCN3CjqW3Z-_coHVNo5K3a3bb9o83hA,109
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- pylocuszoom-0.2.0.dist-info/METADATA,sha256=tDPRbhg4r1NavMCH1e_VTzKY9qApsY97yyiEYh04S78,11723
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- pylocuszoom-0.2.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
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- pylocuszoom-0.2.0.dist-info/licenses/LICENSE.md,sha256=U2y_hv8RcN5lECA3uK88irU3ODUE1TDAPictcmnP0Q4,698
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- pylocuszoom-0.2.0.dist-info/RECORD,,