pylocuszoom 0.1.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

pylocuszoom/recombination.py

@@ -22,7 +22,7 @@ from .logging import logger
 RECOMB_COLOR = "#7FCDFF"  # Light blue
 
 # Data sources by species
-DOG_RECOMB_URL = (
+CANINE_RECOMB_URL = (
     "https://github.com/cflerin/dog_recombination/raw/master/dog_genetic_maps.tar.gz"
 )
 
@@ -177,11 +177,11 @@ def get_default_data_dir() -> Path:
     return base / "snp-scope-plot" / "recombination_maps"
 
 
-def download_dog_recombination_maps(
+def download_canine_recombination_maps(
     output_dir: Optional[str] = None,
     force: bool = False,
 ) -> Path:
-    """Download dog recombination rate maps from Campbell et al. 2016.
+    """Download canine recombination rate maps from Campbell et al. 2016.
 
     Downloads from: https://github.com/cflerin/dog_recombination
 
@@ -213,22 +213,22 @@ def download_dog_recombination_maps(
     # Create output directory
     output_path.mkdir(parents=True, exist_ok=True)
 
-    logger.info("Downloading dog recombination maps from GitHub...")
-    logger.debug(f"Source: {DOG_RECOMB_URL}")
+    logger.info("Downloading canine recombination maps from GitHub...")
+    logger.debug(f"Source: {CANINE_RECOMB_URL}")
 
     with tempfile.TemporaryDirectory() as tmpdir:
         # Download tar.gz file
         tar_path = Path(tmpdir) / "dog_genetic_maps.tar.gz"
 
         try:
-            urllib.request.urlretrieve(DOG_RECOMB_URL, tar_path)
+            urllib.request.urlretrieve(CANINE_RECOMB_URL, tar_path)
         except Exception as e:
             logger.debug(f"urllib download failed: {e}")
             logger.debug("Trying alternative method with requests...")
             try:
                 import requests
 
-                response = requests.get(DOG_RECOMB_URL, timeout=60)
+                response = requests.get(CANINE_RECOMB_URL, timeout=60)
                 response.raise_for_status()
                 tar_path.write_bytes(response.content)
             except ImportError:
@@ -282,14 +282,14 @@ def download_dog_recombination_maps(
 
 def load_recombination_map(
     chrom: int,
-    species: str = "dog",
+    species: str = "canine",
     data_dir: Optional[str] = None,
 ) -> pd.DataFrame:
     """Load recombination map for a specific chromosome.
 
     Args:
-        chrom: Chromosome number (1-38 for dog, 1-18 for cat) or 'X'.
-        species: Species name ('dog', 'cat').
+        chrom: Chromosome number (1-38 for canine, 1-18 for feline) or 'X'.
+        species: Species name ('canine', 'feline').
         data_dir: Directory containing recombination maps.
 
     Returns:
@@ -326,7 +326,7 @@ def get_recombination_rate_for_region(
     chrom: int,
     start: int,
     end: int,
-    species: str = "dog",
+    species: str = "canine",
     data_dir: Optional[str] = None,
     genome_build: Optional[str] = None,
 ) -> pd.DataFrame:
@@ -336,7 +336,7 @@ def get_recombination_rate_for_region(
         chrom: Chromosome number.
         start: Start position (bp).
         end: End position (bp).
-        species: Species name ('dog', 'cat').
+        species: Species name ('canine', 'feline').
         data_dir: Directory containing recombination maps.
         genome_build: Target genome build (e.g., "canfam4"). If specified and
             different from source data (CanFam3.1), coordinates are lifted over.
@@ -345,7 +345,7 @@ def get_recombination_rate_for_region(
         DataFrame with pos and rate columns for the region.
 
     Note:
-        Built-in dog recombination maps are in CanFam3.1 coordinates.
+        Built-in canine recombination maps are in CanFam3.1 coordinates.
         If genome_build="canfam4", positions are automatically lifted over.
         This requires pyliftover: pip install pyliftover
     """
@@ -353,7 +353,7 @@ def get_recombination_rate_for_region(
 
     # Liftover if needed
     build = _normalize_build(genome_build)
-    if species == "dog" and build == "canfam4":
+    if species == "canine" and build == "canfam4":
         logger.debug(f"Lifting over recombination map for chr{chrom} to CanFam4")
         df = liftover_recombination_map(
             df, from_build="canfam3", to_build="canfam4", chrom=chrom

pylocuszoom/utils.py

@@ -29,7 +29,9 @@ def is_spark_dataframe(df: Any) -> bool:
         True if PySpark DataFrame, False otherwise.
     """
     # Check class name to avoid importing pyspark
-    return type(df).__name__ == "DataFrame" and type(df).__module__.startswith("pyspark")
+    return type(df).__name__ == "DataFrame" and type(df).__module__.startswith(
+        "pyspark"
+    )
 
 
 def to_pandas(

{pylocuszoom-0.1.0.dist-info → pylocuszoom-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 0.1.0
+Version: 0.3.0
 Summary: Regional association plots for GWAS results with LD coloring, gene tracks, and recombination rate overlays
 Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
 Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
@@ -19,6 +19,7 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
+Requires-Dist: adjusttext>=0.8
 Requires-Dist: bokeh>=3.8.2
 Requires-Dist: kaleido>=0.2.0
 Requires-Dist: loguru>=0.7.0
@@ -28,14 +29,11 @@ Requires-Dist: pandas>=1.4.0
 Requires-Dist: plotly>=5.0.0
 Requires-Dist: pyliftover>=0.4
 Provides-Extra: all
-Requires-Dist: adjusttext>=0.8; extra == 'all'
 Requires-Dist: pyspark>=3.0.0; extra == 'all'
 Provides-Extra: dev
 Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
 Requires-Dist: pytest>=7.0.0; extra == 'dev'
 Requires-Dist: ruff>=0.1.0; extra == 'dev'
-Provides-Extra: labels
-Requires-Dist: adjusttext>=0.8; extra == 'labels'
 Provides-Extra: spark
 Requires-Dist: pyspark>=3.0.0; extra == 'spark'
 Description-Content-Type: text/markdown
@@ -71,16 +69,24 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
 - **eQTL overlay**: Expression QTL data as separate panel
 - **PySpark support**: Handles large-scale genomics DataFrames
 
+![Example regional association plot](examples/regional_plot.png)
+
 ## Installation
 
+```bash
+pip install pylocuszoom
+```
+
+Or with uv:
+
 ```bash
 uv add pylocuszoom
 ```
 
-Or with pip:
+Or with conda (Bioconda):
 
 ```bash
-pip install pylocuszoom
+conda install -c bioconda pylocuszoom
 ```
 
 ## Quick Start
@@ -88,8 +94,8 @@ pip install pylocuszoom
 ```python
 from pylocuszoom import LocusZoomPlotter
 
-# Initialize plotter (loads reference data for dog)
-plotter = LocusZoomPlotter(species="dog")
+# Initialize plotter (loads reference data for canine)
+plotter = LocusZoomPlotter(species="canine")
 
 # Create regional plot
 fig = plotter.plot(
@@ -109,7 +115,7 @@ fig.savefig("regional_plot.png", dpi=150)
 from pylocuszoom import LocusZoomPlotter
 
 plotter = LocusZoomPlotter(
-    species="dog",                      # or "cat", or None for custom
+    species="canine",                   # or "feline", or None for custom
     plink_path="/path/to/plink",        # Optional, auto-detects if on PATH
 )
 
@@ -134,10 +140,10 @@ fig = plotter.plot(
 
 ## Genome Builds
 
-The default genome build for dog is CanFam3.1. For CanFam4 data:
+The default genome build for canine is CanFam3.1. For CanFam4 data:
 
 ```python
-plotter = LocusZoomPlotter(species="dog", genome_build="canfam4")
+plotter = LocusZoomPlotter(species="canine", genome_build="canfam4")
 ```
 
 Recombination maps are automatically lifted over from CanFam3.1 to CanFam4 coordinates using the UCSC liftOver chain file.
@@ -145,8 +151,8 @@ Recombination maps are automatically lifted over from CanFam3.1 to CanFam4 coord
 ## Using with Other Species
 
 ```python
-# Cat (LD and gene tracks, user provides recombination data)
-plotter = LocusZoomPlotter(species="cat")
+# Feline (LD and gene tracks, user provides recombination data)
+plotter = LocusZoomPlotter(species="feline")
 
 # Custom species (provide all reference data)
 plotter = LocusZoomPlotter(
@@ -163,27 +169,30 @@ fig = plotter.plot(
 )
 ```
 
-## Interactive Backends
+## Backends
 
-Choose between static (matplotlib) and interactive (plotly, bokeh) outputs:
+pyLocusZoom supports multiple rendering backends:
 
 ```python
 # Static publication-quality plot (default)
-plotter = LocusZoomPlotter(species="dog", backend="matplotlib")
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="matplotlib")
 fig.savefig("plot.png", dpi=150)
 
-# Interactive with plotly (hover tooltips, zoom/pan)
-plotter = LocusZoomPlotter(species="dog", backend="plotly")
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
+# Interactive Plotly (hover tooltips, pan/zoom)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="plotly")
 fig.write_html("plot.html")
 
-# Interactive with bokeh (dashboard-friendly)
-plotter = LocusZoomPlotter(species="dog", backend="bokeh")
-fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000)
+# Interactive Bokeh (dashboard-ready)
+fig = plotter.plot(gwas_df, chrom=1, start=1000000, end=2000000, backend="bokeh")
 ```
 
-Interactive plots show SNP details (RS ID, p-value, R²) on hover.
+| Backend | Output | Best For |
+|---------|--------|----------|
+| `matplotlib` | Static PNG/PDF/SVG | Publications, presentations |
+| `plotly` | Interactive HTML | Web reports, data exploration |
+| `bokeh` | Interactive HTML | Dashboards, web apps |
+
+> **Note:** All backends support gene track, recombination overlay, and LD legend. SNP labels (auto-positioned with adjustText) are matplotlib-only.
 
 ## Stacked Plots
 
@@ -324,14 +333,14 @@ chr	pos	rate	cM
 
 ## Reference Data
 
-Dog recombination maps are downloaded from [Campbell et al. 2016](https://github.com/cflerin/dog_recombination) on first use.
+Canine recombination maps are downloaded from [Campbell et al. 2016](https://github.com/cflerin/dog_recombination) on first use.
 
 To manually download:
 
 ```python
-from pylocuszoom import download_dog_recombination_maps
+from pylocuszoom import download_canine_recombination_maps
 
-download_dog_recombination_maps()
+download_canine_recombination_maps()
 ```
 
 ## Logging

pylocuszoom-0.3.0.dist-info/RECORD

@@ -0,0 +1,21 @@
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+pylocuszoom/colors.py,sha256=XXTCmCFfHrOrSiP6b0V8Kis7Z1tyvGEKJpdv59QDVQ8,6610
+pylocuszoom/eqtl.py,sha256=9lZJ8jT1WEj3won6D9B54xdqUvbRvxpOitf97NCUR28,6167
+pylocuszoom/finemapping.py,sha256=PJ4HJYeCaHZecUmADCEGQxKd9HhhjrdIA1H5LQsUmLI,6332
+pylocuszoom/gene_track.py,sha256=CbKqIIl-3VpqIS0NWQ7p-VazhrgbF0-XDkkvoWx_2jI,18665
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+pylocuszoom/ld.py,sha256=64xIulpDVvbMSryWUPoCQ99Odcjwf1wejpwVr_30MLU,6412
+pylocuszoom/logging.py,sha256=nZHEkbnjp8zoyWj_S-Hy9UQvUYLoMoxyiOWRozBT2dg,4987
+pylocuszoom/plotter.py,sha256=7wEN0b3emb0SM7gYn8bSjXBGNt7npw3y3y5AEC-Ha2k,43660
+pylocuszoom/recombination.py,sha256=Q2tAft54nJWHlZt-vZje1r_5RP7D8_VUy5ab_deYXVw,13749
+pylocuszoom/utils.py,sha256=fKNX9WSTbfHR1EpPYijt6ycNjXEjwzunQMHXAvHaK3s,5211
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+pylocuszoom/reference_data/__init__.py,sha256=qqHqAUt1jebGlCN3CjqW3Z-_coHVNo5K3a3bb9o83hA,109
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+pylocuszoom-0.3.0.dist-info/licenses/LICENSE.md,sha256=U2y_hv8RcN5lECA3uK88irU3ODUE1TDAPictcmnP0Q4,698
+pylocuszoom-0.3.0.dist-info/RECORD,,

pylocuszoom-0.1.0.dist-info/RECORD

@@ -1,20 +0,0 @@
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-pylocuszoom/utils.py,sha256=1I4r9KOd8yje12L0Y7GiX2Adc7Qrefq5VqdHv83KM7g,5197
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