pylocuszoom 1.1.2__py3-none-any.whl → 1.3.1__py3-none-any.whl

pylocuszoom/recombination.py

@@ -395,6 +395,45 @@ def get_recombination_rate_for_region(
     return region_df[["pos", "rate"]]
 
 
+def ensure_recomb_maps(
+    species: str = "canine",
+    data_dir: Optional[str] = None,
+) -> Optional[Path]:
+    """Ensure recombination maps are available, downloading if needed.
+
+    Args:
+        species: Species name ('canine', 'feline', etc.).
+        data_dir: Directory for recombination maps. Uses default if None.
+
+    Returns:
+        Path to recombination maps directory, or None if species not supported
+        or download fails.
+    """
+    if species != "canine":
+        logger.debug(f"No built-in recombination maps for species: {species}")
+        return None
+
+    if data_dir is not None:
+        output_path = Path(data_dir)
+    else:
+        output_path = get_default_data_dir()
+
+    # Check if maps already exist
+    if output_path.exists():
+        existing_files = list(output_path.glob("chr*_recomb.tsv"))
+        if len(existing_files) >= 39:  # 38 autosomes + X
+            logger.debug(f"Recombination maps already exist at {output_path}")
+            return output_path
+
+    # Download maps with error handling
+    logger.info("Downloading canine recombination maps...")
+    try:
+        return download_canine_recombination_maps(output_dir=str(output_path))
+    except Exception as e:
+        logger.warning(f"Could not download recombination maps: {e}")
+        return None
+
+
 def add_recombination_overlay(
     ax: Axes,
     recomb_df: pd.DataFrame,

{pylocuszoom-1.1.2.dist-info → pylocuszoom-1.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 1.1.2
+Version: 1.3.1
 Summary: Publication-ready regional association plots with LD coloring, gene tracks, and recombination overlays
 Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
 Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
@@ -35,6 +35,7 @@ Requires-Dist: tqdm>=4.60.0
 Provides-Extra: all
 Requires-Dist: pyspark>=3.0.0; extra == 'all'
 Provides-Extra: dev
+Requires-Dist: hypothesis>=6.0.0; extra == 'dev'
 Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
 Requires-Dist: pytest-randomly>=3.0.0; extra == 'dev'
 Requires-Dist: pytest-xdist>=3.0.0; extra == 'dev'
@@ -71,20 +72,23 @@ Inspired by [LocusZoom](http://locuszoom.org/) and [locuszoomr](https://github.c
     - **SNP labels (matplotlib)**: Automatic labeling of top SNPs by p-value (RS IDs)
     - **Hover tooltips (Plotly and Bokeh)**: Detailed SNP data on hover
 
-![Example regional association plot with LD coloring, gene track, and recombination overlay](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/regional_plot_with_recomb.png)
+![Example regional association plot with LD coloring, gene track, and recombination overlay](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/regional_plot_with_recomb.png)
 *Regional association plot with LD coloring, gene/exon track, recombination rate overlay (blue line), and top SNP labels.*
 
 2. **Stacked plots**: Compare multiple GWAS/phenotypes vertically
-3. **Manhattan plots**: Genome-wide association visualization with chromosome coloring
-4. **QQ plots**: Quantile-quantile plots with confidence bands and genomic inflation factor
-5. **eQTL plot**: Expression QTL data aligned with association plots and gene tracks
-6. **Fine-mapping plots**: Visualize SuSiE credible sets with posterior inclusion probabilities
-7. **PheWAS plots**: Phenome-wide association study visualization across multiple phenotypes
-8. **Forest plots**: Meta-analysis effect size visualization with confidence intervals
-9. **Multiple backends**: matplotlib (publication-ready), plotly (interactive), bokeh (dashboard integration)
-10. **Pandas and PySpark support**: Works with both Pandas and PySpark DataFrames for large-scale genomics data
-11. **Convenience data file loaders**: Load and validate common GWAS, eQTL and fine-mapping file formats
-12. **Automatic gene annotations**: Fetch gene/exon data from Ensembl REST API with caching (human, mouse, rat, canine, feline, and any Ensembl species)
+3. **Miami plots**: Mirrored Manhattan plots for comparing two GWAS datasets (discovery vs replication)
+4. **Manhattan plots**: Genome-wide association visualization with chromosome coloring
+5. **QQ plots**: Quantile-quantile plots with confidence bands and genomic inflation factor
+6. **eQTL plot**: Expression QTL data aligned with association plots and gene tracks
+7. **Fine-mapping plots**: Visualize SuSiE credible sets with posterior inclusion probabilities
+8. **PheWAS plots**: Phenome-wide association study visualization across multiple phenotypes
+9. **Forest plots**: Meta-analysis effect size visualization with confidence intervals
+10. **LD heatmaps**: Triangular heatmaps showing pairwise LD patterns, standalone or integrated below regional plots
+11. **Colocalization plots**: GWAS-eQTL scatter plots with LD coloring, correlation statistics, and effect direction visualization
+12. **Multiple backends**: matplotlib (publication-ready), plotly (interactive), bokeh (dashboard integration)
+12. **Pandas and PySpark support**: Works with both Pandas and PySpark DataFrames for large-scale genomics data
+13. **Convenience data file loaders**: Load and validate common GWAS, eQTL and fine-mapping file formats
+14. **Automatic gene annotations**: Fetch gene/exon data from Ensembl REST API with caching (human, mouse, rat, canine, feline, and any Ensembl species)
 
 ## Installation
 
@@ -254,7 +258,7 @@ fig = plotter.plot_stacked(
 )
 ```
 
-![Example stacked plot comparing two phenotypes](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/stacked_plot.png)
+![Example stacked plot comparing two phenotypes](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/stacked_plot.png)
 *Stacked plot comparing two phenotypes with LD coloring and shared gene track.*
 
 ## eQTL Overlay
@@ -283,7 +287,7 @@ fig = plotter.plot_stacked(
 )
 ```
 
-![Example eQTL overlay plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/eqtl_overlay.png)
+![Example eQTL overlay plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/eqtl_overlay.png)
 *eQTL overlay with effect direction (up/down triangles) and magnitude binning.*
 
 ## Fine-mapping Visualization
@@ -312,28 +316,130 @@ fig = plotter.plot_stacked(
 )
 ```
 
-![Example fine-mapping plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/finemapping_plot.png)
+![Example fine-mapping plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/finemapping_plot.png)
 *Fine-mapping visualization with PIP line and credible set coloring (CS1/CS2).*
 
+## LD Heatmaps
+
+Create triangular LD heatmaps showing pairwise linkage disequilibrium patterns:
+
+```python
+from pylocuszoom import LDHeatmapPlotter
+
+# ld_matrix is a square DataFrame with SNP IDs as index/columns
+# snp_ids is a list of SNP IDs in the matrix
+
+ld_plotter = LDHeatmapPlotter()
+fig = ld_plotter.plot(
+    ld_matrix,
+    snp_ids,
+    highlight_snp_id="rs12345",  # Highlight lead SNP
+    metric="r2",                  # or "dprime"
+)
+fig.savefig("ld_heatmap.png", dpi=150)
+```
+
+![Example LD heatmap](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/ld_heatmap.png)
+*Triangular LD heatmap with R² values and lead SNP highlighted.*
+
+### Integrated LD Heatmap with Regional Plot
+
+Add an LD heatmap panel below a regional association plot:
+
+```python
+from pylocuszoom import LocusZoomPlotter
+
+plotter = LocusZoomPlotter(species="canine")
+
+fig = plotter.plot(
+    gwas_df,
+    chrom=1,
+    start=1000000,
+    end=2000000,
+    lead_pos=1500000,
+    ld_heatmap_df=ld_matrix,         # Pairwise LD matrix
+    ld_heatmap_snp_ids=snp_ids,      # SNP IDs in matrix
+    ld_heatmap_height=0.25,          # Panel height ratio
+)
+```
+
+![Example regional plot with LD heatmap](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/regional_with_ld_heatmap.png)
+*Regional association plot with integrated LD heatmap panel below.*
+
+## Colocalization Plots
+
+Visualize GWAS-eQTL colocalization by comparing association signals in a scatter plot with LD coloring:
+
+```python
+from pylocuszoom import ColocPlotter
+
+# GWAS and eQTL data with matching positions
+gwas_df = pd.DataFrame({
+    "pos": positions,
+    "p": gwas_pvalues,
+    "ld_r2": ld_values,  # Optional: LD with lead SNP
+})
+
+eqtl_df = pd.DataFrame({
+    "pos": positions,
+    "p": eqtl_pvalues,
+})
+
+plotter = ColocPlotter()
+fig = plotter.plot_coloc(
+    gwas_df=gwas_df,
+    eqtl_df=eqtl_df,
+    pos_col="pos",
+    gwas_p_col="p",
+    eqtl_p_col="p",
+    ld_col="ld_r2",
+    gwas_threshold=5e-8,
+    eqtl_threshold=1e-5,
+)
+fig.savefig("colocalization.png", dpi=150)
+```
+
+![Example colocalization plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/colocalization_plot.png)
+*GWAS-eQTL colocalization scatter plot with LD coloring and correlation statistics.*
+
+**Advanced options** include effect direction coloring and H4 posterior probability display:
+
+```python
+fig = plotter.plot_coloc(
+    gwas_df=gwas_df,
+    eqtl_df=eqtl_df,
+    pos_col="pos",
+    gwas_p_col="p",
+    eqtl_p_col="p",
+    gwas_effect_col="beta",
+    eqtl_effect_col="slope",
+    color_by_effect=True,  # Green=congruent, Red=incongruent
+    h4_posterior=0.85,     # Display coloc H4 probability
+)
+```
+
 ## PheWAS Plots
 
 Visualize associations of a single variant across multiple phenotypes:
 
 ```python
+from pylocuszoom import StatsPlotter
+
 phewas_df = pd.DataFrame({
     "phenotype": ["Height", "BMI", "T2D", "CAD", "HDL"],
     "p_value": [1e-15, 0.05, 1e-8, 1e-3, 1e-10],
     "category": ["Anthropometric", "Anthropometric", "Metabolic", "Cardiovascular", "Lipids"],
 })
 
-fig = plotter.plot_phewas(
+stats_plotter = StatsPlotter()
+fig = stats_plotter.plot_phewas(
     phewas_df,
     variant_id="rs12345",
     category_col="category",
 )
 ```
 
-![Example PheWAS plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/phewas_plot.png)
+![Example PheWAS plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/phewas_plot.png)
 *PheWAS plot showing associations across phenotype categories with significance threshold.*
 
 ## Forest Plots
@@ -341,6 +447,8 @@ fig = plotter.plot_phewas(
 Create forest plots for meta-analysis visualization:
 
 ```python
+from pylocuszoom import StatsPlotter
+
 forest_df = pd.DataFrame({
     "study": ["Study A", "Study B", "Study C", "Meta-analysis"],
     "effect": [0.45, 0.52, 0.38, 0.46],
@@ -349,24 +457,68 @@ forest_df = pd.DataFrame({
     "weight": [25, 35, 20, 100],
 })
 
-fig = plotter.plot_forest(
+stats_plotter = StatsPlotter()
+fig = stats_plotter.plot_forest(
     forest_df,
     variant_id="rs12345",
     weight_col="weight",
 )
 ```
 
-![Example forest plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/forest_plot.png)
+![Example forest plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/forest_plot.png)
 *Forest plot with effect sizes, confidence intervals, and weight-proportional markers.*
 
+## Miami Plots
+
+Compare two GWAS datasets with mirrored Manhattan plots (top panel ascending, bottom panel inverted):
+
+```python
+from pylocuszoom import MiamiPlotter
+
+plotter = MiamiPlotter(species="human")
+
+fig = plotter.plot_miami(
+    discovery_df,
+    replication_df,
+    chrom_col="chrom",
+    pos_col="pos",
+    p_col="p",
+    top_label="Discovery",
+    bottom_label="Replication",
+    top_threshold=5e-8,
+    bottom_threshold=1e-6,
+    highlight_regions=[("6", 30_000_000, 35_000_000)],  # Highlight MHC region
+)
+fig.savefig("miami.png", dpi=150)
+```
+
+**Interactive backends** (Plotly/Bokeh) provide hover tooltips showing SNP details:
+
+```python
+# Plotly - interactive HTML with hover tooltips
+plotter = MiamiPlotter(species="human", backend="plotly")
+fig = plotter.plot_miami(discovery_df, replication_df, ...)
+fig.write_html("miami_interactive.html")
+
+# Bokeh - dashboard-ready interactive plots
+from bokeh.io import output_file, save
+plotter = MiamiPlotter(species="human", backend="bokeh")
+fig = plotter.plot_miami(discovery_df, replication_df, ...)
+output_file("miami_bokeh.html")
+save(fig)
+```
+
+![Example Miami plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/miami_plot.png)
+*Miami plot comparing discovery and replication GWAS with mirrored y-axes and region highlighting.*
+
 ## Manhattan Plots
 
 Create genome-wide Manhattan plots showing associations across all chromosomes:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter(species="human")
+plotter = ManhattanPlotter(species="human")
 
 fig = plotter.plot_manhattan(
     gwas_df,
@@ -379,7 +531,7 @@ fig = plotter.plot_manhattan(
 fig.savefig("manhattan.png", dpi=150)
 ```
 
-![Example Manhattan plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/manhattan_plot.png)
+![Example Manhattan plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/manhattan_plot.png)
 *Manhattan plot showing genome-wide associations with chromosome coloring and significance threshold.*
 
 Categorical Manhattan plots (PheWAS-style) are also supported:
@@ -397,9 +549,9 @@ fig = plotter.plot_manhattan(
 Create quantile-quantile plots to assess p-value distribution:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_qq(
     gwas_df,
@@ -411,7 +563,7 @@ fig = plotter.plot_qq(
 fig.savefig("qq_plot.png", dpi=150)
 ```
 
-![Example QQ plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/qq_plot.png)
+![Example QQ plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/qq_plot.png)
 *QQ plot with 95% confidence band and genomic inflation factor (λ).*
 
 ## Stacked Manhattan Plots
@@ -419,9 +571,9 @@ fig.savefig("qq_plot.png", dpi=150)
 Compare multiple GWAS results in vertically stacked Manhattan plots:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_manhattan_stacked(
     [gwas_study1, gwas_study2, gwas_study3],
@@ -436,7 +588,7 @@ fig = plotter.plot_manhattan_stacked(
 fig.savefig("manhattan_stacked.png", dpi=150)
 ```
 
-![Example stacked Manhattan plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/manhattan_stacked.png)
+![Example stacked Manhattan plot](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/manhattan_stacked.png)
 *Stacked Manhattan plots comparing three GWAS studies with shared chromosome axis.*
 
 ## Manhattan and QQ Side-by-Side
@@ -444,9 +596,9 @@ fig.savefig("manhattan_stacked.png", dpi=150)
 Create combined Manhattan and QQ plots in a single figure:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_manhattan_qq(
     gwas_df,
@@ -462,7 +614,7 @@ fig = plotter.plot_manhattan_qq(
 fig.savefig("manhattan_qq.png", dpi=150)
 ```
 
-![Example Manhattan and QQ side-by-side](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/manhattan_qq_sidebyside.png)
+![Example Manhattan and QQ side-by-side](https://raw.githubusercontent.com/michael-denyer/pyLocusZoom/main/examples/matplotlib/manhattan_qq_sidebyside.png)
 *Combined Manhattan and QQ plot showing genome-wide associations and p-value distribution.*
 
 ## PySpark Support

{pylocuszoom-1.1.2.dist-info → pylocuszoom-1.3.1.dist-info}/RECORD

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