pylocuszoom 1.1.2__tar.gz → 1.2.0__tar.gz

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/.gitignore

@@ -14,6 +14,7 @@ build/
 .benchmarks/
 .coverage
 htmlcov/
+.hypothesis/
 
 # IDE
 .idea/
@@ -21,6 +22,9 @@ htmlcov/
 *.swp
 .claude/
 
+# Git worktrees
+.worktrees/
+
 # Issue tracking (local)
 .beads/
 

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/CHANGELOG.md

@@ -5,6 +5,30 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+## [1.2.0] - 2026-02-02
+
+### Added
+
+- Property-based testing with Hypothesis library for improved test coverage
+- `tests/strategies.py` module with reusable GWAS data generators
+- Hypothesis test profiles (ci/dev/debug) for configurable test intensity
+- Property tests for validation, colors, plotter, gene track, Manhattan, and QQ modules
+- `ensure_recomb_maps()` function exported from package for pre-downloading recombination data
+- `plot_finemapping()` function exported from package for standalone fine-mapping plots
+
+### Changed
+
+- **BREAKING**: Removed deprecated wrapper methods from `LocusZoomPlotter`
+  - Removed: `plot_manhattan()`, `plot_qq()`, `plot_manhattan_stacked()`, `plot_manhattan_qq()`, `plot_manhattan_qq_stacked()` — use `ManhattanPlotter` instead
+  - Removed: `plot_phewas()`, `plot_forest()` — use `StatsPlotter` instead
+
+### Internal
+
+- Test count increased from 667 to 690 with hypothesis property tests
+- Removed unused `OPTIONAL_FINEMAPPING_COLS` constant from finemapping module
+
 ## [1.1.2] - 2026-01-30
 
 ### Fixed
@@ -271,6 +295,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - bokeh >= 3.8.2
 - kaleido >= 0.2.0
 
+[1.2.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v1.1.2...v1.2.0
 [1.1.2]: https://github.com/michael-denyer/pyLocusZoom/compare/v1.1.1...v1.1.2
 [1.1.1]: https://github.com/michael-denyer/pyLocusZoom/compare/v1.1.0...v1.1.1
 [1.1.0]: https://github.com/michael-denyer/pyLocusZoom/compare/v1.0.2...v1.1.0

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 1.1.2
+Version: 1.2.0
 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'
@@ -320,13 +321,16 @@ fig = plotter.plot_stacked(
 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",
@@ -341,6 +345,8 @@ 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],
@@ -349,7 +355,8 @@ 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",
@@ -364,9 +371,9 @@ fig = plotter.plot_forest(
 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,
@@ -397,9 +404,9 @@ 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,
@@ -419,9 +426,9 @@ 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],
@@ -444,9 +451,9 @@ 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,

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/README.md

@@ -274,13 +274,16 @@ fig = plotter.plot_stacked(
 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",
@@ -295,6 +298,8 @@ 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],
@@ -303,7 +308,8 @@ 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",
@@ -318,9 +324,9 @@ fig = plotter.plot_forest(
 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,
@@ -351,9 +357,9 @@ 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,
@@ -373,9 +379,9 @@ 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],
@@ -398,9 +404,9 @@ 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,

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/docs/USER_GUIDE.md

@@ -27,13 +27,6 @@ Comprehensive documentation for pyLocusZoom - regional association plots for GWA
   - [LocusZoomPlotter](#locuszoomplotter)
   - [plot() Method](#plot-method)
   - [plot_stacked() Method](#plot_stacked-method)
-  - [plot_manhattan() Method](#plot_manhattan-method)
-  - [plot_qq() Method](#plot_qq-method)
-  - [plot_manhattan_stacked() Method](#plot_manhattan_stacked-method)
-  - [plot_manhattan_qq() Method](#plot_manhattan_qq-method)
-  - [plot_manhattan_qq_stacked() Method](#plot_manhattan_qq_stacked-method)
-  - [plot_phewas() Method](#plot_phewas-method)
-  - [plot_forest() Method](#plot_forest-method)
 - [File Loaders](#file-loaders)
   - [GWAS Loaders](#gwas-loaders)
   - [eQTL Loaders](#eqtl-loaders)
@@ -231,12 +224,15 @@ Visualize associations of a single variant across multiple phenotypes in a pheno
 ![PheWAS plot](../examples/phewas_plot.png)
 
 ```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"],
 })
 
+plotter = StatsPlotter()
 fig = plotter.plot_phewas(
     phewas_df,
     variant_id="rs12345",
@@ -258,6 +254,8 @@ Create forest plots for meta-analysis visualization showing effect sizes with co
 ![Forest plot](../examples/forest_plot.png)
 
 ```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],
@@ -266,6 +264,7 @@ forest_df = pd.DataFrame({
     "weight": [25, 35, 20, 100],  # Optional: affects marker size
 })
 
+plotter = StatsPlotter()
 fig = plotter.plot_forest(
     forest_df,
     variant_id="rs12345",
@@ -288,6 +287,9 @@ Genome-wide Manhattan plots showing associations across all chromosomes.
 ![Manhattan plot](../examples/manhattan_plot.png)
 
 ```python
+from pylocuszoom import ManhattanPlotter
+
+plotter = ManhattanPlotter()
 fig = plotter.plot_manhattan(
     gwas_df,
     chrom_col="chrom",
@@ -312,6 +314,9 @@ Quantile-quantile plots for assessing p-value distribution and detecting systema
 ![QQ plot](../examples/qq_plot.png)
 
 ```python
+from pylocuszoom import ManhattanPlotter
+
+plotter = ManhattanPlotter()
 fig = plotter.plot_qq(
     gwas_df,
     p_col="p",
@@ -335,6 +340,9 @@ Compare multiple GWAS studies in vertically stacked Manhattan plots with shared
 ![Stacked Manhattan plot](../examples/manhattan_stacked.png)
 
 ```python
+from pylocuszoom import ManhattanPlotter
+
+plotter = ManhattanPlotter()
 fig = plotter.plot_manhattan_stacked(
     [gwas_study1, gwas_study2, gwas_study3],
     chrom_col="chrom",
@@ -362,6 +370,9 @@ Combined Manhattan and QQ plots in a single figure for comprehensive GWAS summar
 ![Manhattan and QQ side-by-side](../examples/manhattan_qq_sidebyside.png)
 
 ```python
+from pylocuszoom import ManhattanPlotter
+
+plotter = ManhattanPlotter()
 fig = plotter.plot_manhattan_qq(
     gwas_df,
     chrom_col="chrom",
@@ -448,6 +459,32 @@ save(fig)
 
 ## API Reference
 
+### Specialized Plotter Classes
+
+pyLocusZoom provides specialized plotter classes for different plot types:
+
+| Class | Purpose |
+|-------|---------|
+| `LocusZoomPlotter` | Regional association plots with LD coloring |
+| `ManhattanPlotter` | Genome-wide Manhattan and QQ plots |
+| `StatsPlotter` | PheWAS and forest plots |
+
+```python
+from pylocuszoom import LocusZoomPlotter, ManhattanPlotter, StatsPlotter
+
+# Regional plots
+regional = LocusZoomPlotter(species="canine")
+fig = regional.plot(gwas_df, chrom=1, start=1e6, end=2e6)
+
+# Manhattan/QQ plots
+manhattan = ManhattanPlotter()
+fig = manhattan.plot_manhattan(gwas_df)
+
+# PheWAS/forest plots
+stats = StatsPlotter()
+fig = stats.plot_phewas(phewas_df, variant_id="rs12345")
+```
+
 ### LocusZoomPlotter
 
 The main class for creating regional association plots.
@@ -582,210 +619,6 @@ fig = plotter.plot_stacked(
 | `finemapping_cs_col` | str | `"cs"` | Column for credible set assignment. |
 | `recomb_df` | DataFrame | None | Custom recombination data. |
 
-### plot_manhattan() Method
-
-Create a genome-wide Manhattan plot showing associations across all chromosomes.
-
-```python
-fig = plotter.plot_manhattan(
-    gwas_df,                        # Required: GWAS results
-    chrom_col="chrom",              # Chromosome column
-    pos_col="pos",                  # Position column
-    p_col="p",                      # P-value column
-    custom_chrom_order=None,        # Custom chromosome order
-    significance_threshold=5e-8,    # Genome-wide significance line
-    figsize=(12, 5),                # Figure dimensions
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `gwas_df` | DataFrame | Required | GWAS results with chromosome, position, and p-value columns. |
-| `chrom_col` | str | `"chrom"` | Chromosome column name. |
-| `pos_col` | str | `"pos"` | Position column name. |
-| `p_col` | str | `"p"` | P-value column name. |
-| `custom_chrom_order` | list | None | Custom order for chromosomes (e.g., `["1", "2", ..., "X"]`). |
-| `significance_threshold` | float | `5e-8` | P-value threshold for significance line. |
-| `figsize` | tuple | `(12, 5)` | Figure dimensions (width, height). |
-
-### plot_qq() Method
-
-Create a quantile-quantile (QQ) plot to assess p-value distribution.
-
-```python
-fig = plotter.plot_qq(
-    gwas_df,                        # Required: GWAS results
-    p_col="p",                      # P-value column
-    show_confidence_band=True,      # 95% confidence band
-    show_lambda=True,               # Genomic inflation factor
-    figsize=(6, 6),                 # Figure dimensions
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `gwas_df` | DataFrame | Required | GWAS results with p-value column. |
-| `p_col` | str | `"p"` | P-value column name. |
-| `show_confidence_band` | bool | `True` | Whether to show 95% confidence band. |
-| `show_lambda` | bool | `True` | Whether to show genomic inflation factor (λ) in title. |
-| `figsize` | tuple | `(6, 6)` | Figure dimensions (width, height). |
-
-### plot_manhattan_stacked() Method
-
-Create stacked Manhattan plots for comparing multiple GWAS studies.
-
-```python
-fig = plotter.plot_manhattan_stacked(
-    gwas_dfs,                       # Required: list of GWAS DataFrames
-    chrom_col="chrom",              # Chromosome column
-    pos_col="pos",                  # Position column
-    p_col="p",                      # P-value column
-    custom_chrom_order=None,        # Custom chromosome order
-    significance_threshold=5e-8,    # Genome-wide significance line
-    panel_labels=None,              # Labels for each panel
-    figsize=(12, 8),                # Figure dimensions
-    title=None,                     # Overall figure title
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `gwas_dfs` | list | Required | List of GWAS DataFrames. |
-| `chrom_col` | str | `"chrom"` | Chromosome column name. |
-| `pos_col` | str | `"pos"` | Position column name. |
-| `p_col` | str | `"p"` | P-value column name. |
-| `custom_chrom_order` | list | None | Custom order for chromosomes. |
-| `significance_threshold` | float | `5e-8` | P-value threshold for significance line. |
-| `panel_labels` | list | None | Labels for each panel (defaults to "Study 1", "Study 2", etc.). |
-| `figsize` | tuple | `(12, 8)` | Figure dimensions (width, height). |
-| `title` | str | None | Overall figure title (suptitle). |
-
-### plot_manhattan_qq() Method
-
-Create a combined Manhattan and QQ plot side-by-side in a single figure.
-
-```python
-fig = plotter.plot_manhattan_qq(
-    gwas_df,                        # Required: GWAS results
-    chrom_col="chrom",              # Chromosome column
-    pos_col="pos",                  # Position column
-    p_col="p",                      # P-value column
-    custom_chrom_order=None,        # Custom chromosome order
-    significance_threshold=5e-8,    # Genome-wide significance line
-    show_confidence_band=True,      # 95% confidence band on QQ
-    show_lambda=True,               # Genomic inflation factor on QQ
-    figsize=(14, 5),                # Figure dimensions
-    title=None,                     # Overall figure title
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `gwas_df` | DataFrame | Required | GWAS results with chromosome, position, and p-value columns. |
-| `chrom_col` | str | `"chrom"` | Chromosome column name. |
-| `pos_col` | str | `"pos"` | Position column name. |
-| `p_col` | str | `"p"` | P-value column name. |
-| `custom_chrom_order` | list | None | Custom order for chromosomes. |
-| `significance_threshold` | float | `5e-8` | P-value threshold for significance line. |
-| `show_confidence_band` | bool | `True` | Whether to show 95% confidence band on QQ plot. |
-| `show_lambda` | bool | `True` | Whether to show genomic inflation factor (λ) on QQ plot. |
-| `figsize` | tuple | `(14, 5)` | Figure dimensions (width, height). |
-| `title` | str | None | Overall figure title (suptitle). |
-
-### plot_manhattan_qq_stacked() Method
-
-Create stacked Manhattan+QQ plot pairs for comparing multiple GWAS studies.
-
-```python
-fig = plotter.plot_manhattan_qq_stacked(
-    gwas_dfs,                       # Required: list of GWAS DataFrames
-    chrom_col="chrom",              # Chromosome column
-    pos_col="pos",                  # Position column
-    p_col="p",                      # P-value column
-    custom_chrom_order=None,        # Custom chromosome order
-    significance_threshold=5e-8,    # Genome-wide significance line
-    show_confidence_band=True,      # 95% confidence band on QQ
-    show_lambda=True,               # Genomic inflation factor on QQ
-    panel_labels=None,              # Labels for each study
-    figsize=(14, 8),                # Figure dimensions
-    title=None,                     # Overall figure title
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `gwas_dfs` | list | Required | List of GWAS DataFrames to compare. |
-| `chrom_col` | str | `"chrom"` | Chromosome column name. |
-| `pos_col` | str | `"pos"` | Position column name. |
-| `p_col` | str | `"p"` | P-value column name. |
-| `custom_chrom_order` | list | None | Custom order for chromosomes. |
-| `significance_threshold` | float | `5e-8` | P-value threshold for significance line. |
-| `show_confidence_band` | bool | `True` | Whether to show 95% confidence band on QQ plots. |
-| `show_lambda` | bool | `True` | Whether to show genomic inflation factor (λ) on QQ plots. |
-| `panel_labels` | list | None | Labels for each panel (defaults to "Study 1", "Study 2", etc.). |
-| `figsize` | tuple | `(14, 8)` | Figure dimensions (width, height). |
-| `title` | str | None | Overall figure title (suptitle). |
-
-### plot_phewas() Method
-
-Create a PheWAS (Phenome-Wide Association Study) plot.
-
-```python
-fig = plotter.plot_phewas(
-    phewas_df,                      # Required: PheWAS results
-    variant_id="rs12345",           # Required: variant ID for title
-    phenotype_col="phenotype",      # Phenotype name column
-    p_col="p_value",                # P-value column
-    category_col="category",        # Category for grouping/coloring
-    effect_col=None,                # Effect column for direction markers
-    significance_threshold=5e-8,    # Significance line threshold
-    figsize=(10, 8),                # Figure dimensions
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `phewas_df` | DataFrame | Required | PheWAS results with phenotype and p-value. |
-| `variant_id` | str | Required | Variant ID for plot title. |
-| `phenotype_col` | str | `"phenotype"` | Column with phenotype names. |
-| `p_col` | str | `"p_value"` | Column with p-values. |
-| `category_col` | str | `"category"` | Column for phenotype categories. |
-| `effect_col` | str | None | Column with effect sizes for direction markers. |
-| `significance_threshold` | float | `5e-8` | P-value for significance line. |
-| `figsize` | tuple | `(10, 8)` | Figure dimensions (width, height). |
-
-### plot_forest() Method
-
-Create a forest plot for meta-analysis visualization.
-
-```python
-fig = plotter.plot_forest(
-    forest_df,                      # Required: meta-analysis data
-    variant_id="rs12345",           # Required: variant ID for title
-    study_col="study",              # Study/phenotype name column
-    effect_col="effect",            # Effect size column
-    ci_lower_col="ci_lower",        # Lower CI column
-    ci_upper_col="ci_upper",        # Upper CI column
-    weight_col=None,                # Optional weight column for marker sizes
-    null_value=0.0,                 # Null effect value (0 for beta, 1 for OR)
-    effect_label="Effect Size",     # X-axis label
-    figsize=(8, 6),                 # Figure dimensions
-)
-```
-
-| Parameter | Type | Default | Description |
-|-----------|------|---------|-------------|
-| `forest_df` | DataFrame | Required | Forest plot data with effects and CIs. |
-| `variant_id` | str | Required | Variant ID for plot title. |
-| `study_col` | str | `"study"` | Column with study/phenotype names. |
-| `effect_col` | str | `"effect"` | Column with effect sizes. |
-| `ci_lower_col` | str | `"ci_lower"` | Column with lower confidence interval. |
-| `ci_upper_col` | str | `"ci_upper"` | Column with upper confidence interval. |
-| `weight_col` | str | None | Column with study weights (affects marker size). |
-| `null_value` | float | `0.0` | Reference value for null effect line. |
-| `effect_label` | str | `"Effect Size"` | X-axis label. |
-| `figsize` | tuple | `(8, 6)` | Figure dimensions (width, height). |
-
 ### Parameter Naming Conventions
 
 Note the difference in parameter naming between single-region and multi-region methods:

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/examples/generate_example_plots.py

@@ -13,7 +13,7 @@ matplotlib.use("Agg")  # Non-interactive backend
 import numpy as np
 import pandas as pd
 
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import LocusZoomPlotter, ManhattanPlotter, StatsPlotter
 
 
 def generate_p_values(
@@ -814,7 +814,8 @@ phewas_df = pd.DataFrame(
         ],
     }
 )
-fig = plotter.plot_phewas(phewas_df, variant_id="rs7903146")
+stats_plotter = StatsPlotter()
+fig = stats_plotter.plot_phewas(phewas_df, variant_id="rs7903146")
 fig.savefig("examples/phewas_plot.png", dpi=150, bbox_inches="tight")
 print("   Saved: examples/phewas_plot.png")
 
@@ -838,7 +839,7 @@ forest_df = pd.DataFrame(
         "weight": [22, 18, 8, 28, 12, 12, 100],
     }
 )
-fig = plotter.plot_forest(
+fig = stats_plotter.plot_forest(
     forest_df,
     variant_id="rs7903146 (TCF7L2)",
     weight_col="weight",
@@ -868,7 +869,7 @@ for chrom in range(1, 23):
 
 manhattan_df = pd.DataFrame(manhattan_data)
 
-manhattan_plotter = LocusZoomPlotter(species="human", log_level=None)
+manhattan_plotter = ManhattanPlotter(species="human")
 fig = manhattan_plotter.plot_manhattan(
     manhattan_df,
     significance_threshold=5e-8,
@@ -890,7 +891,7 @@ qq_pvalues[:n_true] = 10 ** np.random.uniform(-10, -5, n_true)
 
 qq_df = pd.DataFrame({"p": qq_pvalues})
 
-qq_plotter = LocusZoomPlotter(log_level=None)
+qq_plotter = ManhattanPlotter()
 fig = qq_plotter.plot_qq(
     qq_df,
     show_confidence_band=True,
@@ -902,9 +903,7 @@ print("   Saved: examples/qq_plot.png")
 
 # Interactive Plotly Manhattan plot
 print("20. Interactive Plotly Manhattan plot...")
-manhattan_plotter_plotly = LocusZoomPlotter(
-    species="human", backend="plotly", log_level=None
-)
+manhattan_plotter_plotly = ManhattanPlotter(species="human", backend="plotly")
 fig = manhattan_plotter_plotly.plot_manhattan(
     manhattan_df,
     significance_threshold=5e-8,
@@ -919,9 +918,7 @@ print("21. Interactive Bokeh Manhattan plot...")
 from bokeh.io import save
 from bokeh.resources import CDN
 
-manhattan_plotter_bokeh = LocusZoomPlotter(
-    species="human", backend="bokeh", log_level=None
-)
+manhattan_plotter_bokeh = ManhattanPlotter(species="human", backend="bokeh")
 fig = manhattan_plotter_bokeh.plot_manhattan(
     manhattan_df,
     significance_threshold=5e-8,
@@ -935,7 +932,7 @@ print("   Saved: examples/manhattan_bokeh.html")
 
 # Interactive Plotly QQ plot
 print("22. Interactive Plotly QQ plot...")
-qq_plotter_plotly = LocusZoomPlotter(backend="plotly", log_level=None)
+qq_plotter_plotly = ManhattanPlotter(backend="plotly")
 fig = qq_plotter_plotly.plot_qq(
     qq_df,
     show_confidence_band=True,
@@ -947,7 +944,7 @@ print("   Saved: examples/qq_plotly.html")
 
 # Interactive Bokeh QQ plot
 print("23. Interactive Bokeh QQ plot...")
-qq_plotter_bokeh = LocusZoomPlotter(backend="bokeh", log_level=None)
+qq_plotter_bokeh = ManhattanPlotter(backend="bokeh")
 fig = qq_plotter_bokeh.plot_qq(
     qq_df,
     show_confidence_band=True,

{pylocuszoom-1.1.2 → pylocuszoom-1.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pylocuszoom"
-version = "1.1.2"
+version = "1.2.0"
 description = "Publication-ready regional association plots with LD coloring, gene tracks, and recombination overlays"
 readme = "README.md"
 license = "GPL-3.0-or-later"
@@ -46,6 +46,7 @@ dev = [
     "pytest-cov>=4.0.0",
     "pytest-randomly>=3.0.0",
     "pytest-xdist>=3.0.0",
+    "hypothesis>=6.0.0",
     "ruff>=0.1.0",
 ]
 spark = [