pycmplot 0.2.9__tar.gz → 0.3.1__tar.gz

{pycmplot-0.2.9 → pycmplot-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycmplot
-Version: 0.2.9
+Version: 0.3.1
 Summary: Multi-track circular and linear Manhattan plot generation for GWAS summary statistics
 Author: Kevin Esoh
 Author-email: Kevin Esoh <kesohku1@jh.edu>
@@ -39,16 +39,56 @@ Dynamic: license-file
 
 # pycmplot
 
-Multi-track **circular** and **linear** Manhattan plot generation for GWAS summary statistics.
+<div>
+  <h1 align="center">Multi-track circular and linear Manhattan plotting in Python.</h1>
+</div>
+
+<p align="center">
+  <img width="600" height="400" src="docs/pycmplot-logo-circular.png">
+</p>
+
 
 ```
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
-|  PACKAGE FOR CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
-|                    Kevin Esoh, 2026                  |
-|                    kesohku1@jh.edu                   |
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    |  MULTI-TRACK CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
+                    |                      in Python                       |
+                    |                    Kevin Esoh, 2026                  |
+                    |                    kesohku1@jh.edu                   |
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ```
 
+----------------------------------------------
+
+## Content
+1. [Overview](#overview)
+2. [Key features](#key-features)
+    - [Column auto-detection](#column-auto-detection)
+    - [Density-aware sub-sampling](#density-aware-sub-sampling)
+    - [Trim insignificant variants for faster plotting](#trim-insignificant-variants-for-faster-plotting)
+    - [Genome build conversion (liftover)](#genome-build-conversion-liftover)
+    - [Nearest-gene annotation for GWAS lead SNPs](#nearest-gene-annotation-for-gwas-lead-snps)
+3. [Application](#application)
+4. [Tip](#tip)
+5. [Installation](#installation)
+    - [From PyPI](#from-pypi)
+    - [From GitHub](#from-github)
+    - [Python virtual environment](#python-virtual-environment)
+6. [Test the installation](#test-the-installation)
+7. [Dependencies](#dependencies)
+8. [Command-line usage](#command-line-usage)
+    - [Linear Manhattan (default)](#linear-manhattan-default)
+    - [Circular Manhattan](#circular-manhattan)
+    - [Key options](#key-options)
+9. [Python API](#python-api)
+10. [Contributing](#contributing)
+11. [Contributors](#contributors)
+
+
+---------------------------------------------
+
+
+## Overview 
+
 This package will take any number of per SNP/variant summary statistics, be it GWAS, 
 selection scans (e.g. iHS, EHH, FST), etc and generate Manhattan plots. If given a single
 file, a single one-track Manhattan plot will be generated. Multiple files will result in 
@@ -68,8 +108,8 @@ option of the package should be used to indicate the column and then the package
 postions in hg19 to hg38 ensuring that hits table generation and plotting are done with one unified 
 corrdinate system.
 
-# Key features
-## Column auto-detection
+## Key features
+### Column auto-detection
 A key functionality of the package is its ability to auto-detect certain columns if ommited on the 
 command-line or python API:
 - Chromosome column: `-chr, --chrom_column` or ommited
@@ -92,7 +132,7 @@ bld_candidates = [build, 'BUILD', 'Genome', 'Genome_Build', 'Genome-build']
 
 > NB: Upper and lower cases of the candidates are also considered, making each candidate expanded 3 times.
 
-## Density-aware sub-sampling
+### Density-aware sub-sampling
 Another key feature is density-aware sub-sampling for Manhattan-style scatter plots.
 This was inspired by ``gwaslab``'s default behaviour (https://cloufield.github.io/gwaslab/). 
 
@@ -103,14 +143,14 @@ scan with the defaults below, this typically cuts the plotted point count from 1
 to ~200 K + a few hundred peaks — visually indistinguishable above the suggestive 
 band, but two orders of magnitude faster to render.
 
-## Trim insignificant variants for faster plotting
+### Trim insignificant variants for faster plotting
 An optional parameter `-tp, --trim_pval` is provided to increase speed even further. 
 Set with a value to exclude variants with p-value above a certain threshold, 
 e.g. `0.01 (1e-2)` or `0.001 (1e-3)`. Performed on top of the default auto-thin 
 feature above, it siginificant increases speed and reduces peak memory usage. 
 See benchmark figure (manuscript in preparation).
 
-## Genome build conversion (liftover)
+### Genome build conversion (liftover)
 Conversion of a both hg18 and hg19 positions to their hg38 equivalent is included through
 `pyliftover.LiftOver`.
 
@@ -120,7 +160,7 @@ column to specify the genome build of each position ('hg18', 'hg19', or 'hg38')
 using one coordinate system. If only 'hg18' or 'hg19' positions are present, no liftover 
 be necessary. Hence, liftover is only performed in cases of mixed genome builds.
 
-## Nearest-gene annotation for GWAS lead SNPs
+### Nearest-gene annotation for GWAS lead SNPs
 The package bundles GFF3 files in hg19 and hg38 coordinates processed to reduce size 
 for gene annotation. Also included are UCSC chain files for coordinate conversion (liftover).
   - ``chain_hg19_hg38`` -- UCSC LiftOver chain file for hg19 to hg38
@@ -139,12 +179,12 @@ for gene annotation. Also included are UCSC chain files for coordinate conversio
     ``Homo_sapiens.GRCh37.geneinfo.tsv.gz``.
 
 
-# Application
+## Application
 A potential useful application is **comparative visualization** of results from multiple imputation panels, 
 multiple populations, or multiple traits to observe shared genetic architecture.
 
 
-# Tip
+## Tip
 
 For signed non-pvalue statistics such as iHS, use `--signif_threshold` and 
 `--suggest_threshold` to specify lines to draw for iHS cutoff above and below zero, 
@@ -153,7 +193,7 @@ that is in the positive and negative axes.
 
 Read more in the package documentation page: https://pycmplot.readthedocs.io/en/latest/
 
----
+----------------------------
 
 ## Installation
 
@@ -180,24 +220,25 @@ pip install -e . --break-system-packages
 ```
 
 
-### Use python virtual environment if local installation is not possible
-```bash
-python -m venv ~/bin/pycmplot
+### Python virtual environment
 
-source ~/bin/pycmplot/bin/activate
+Use python virtual environment if local installation is not possible
 
-pip install --upgrade pip setuptools wheel
+```bash
+python -m venv ~/envs/pycmplot
+source ~/envs/pycmplot/bin/activate
 
-# then follow any of the installation steps above
+pip install --upgrade pip setuptools wheel
+pip install pycmplot
 ```
 
 
-# Test the installation
+## Test the installation
 ```bash
 pycmplot -h
 ```
 
-### Dependencies
+## Dependencies
 
 | Package | Purpose |
 |---------|---------|

{pycmplot-0.2.9 → pycmplot-0.3.1}/README.md

@@ -1,15 +1,55 @@
 # pycmplot
 
-Multi-track **circular** and **linear** Manhattan plot generation for GWAS summary statistics.
+<div>
+  <h1 align="center">Multi-track circular and linear Manhattan plotting in Python.</h1>
+</div>
+
+<p align="center">
+  <img width="600" height="400" src="docs/pycmplot-logo-circular.png">
+</p>
+
 
 ```
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
-|  PACKAGE FOR CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
-|                    Kevin Esoh, 2026                  |
-|                    kesohku1@jh.edu                   |
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    |  MULTI-TRACK CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
+                    |                      in Python                       |
+                    |                    Kevin Esoh, 2026                  |
+                    |                    kesohku1@jh.edu                   |
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ```
 
+----------------------------------------------
+
+## Content
+1. [Overview](#overview)
+2. [Key features](#key-features)
+    - [Column auto-detection](#column-auto-detection)
+    - [Density-aware sub-sampling](#density-aware-sub-sampling)
+    - [Trim insignificant variants for faster plotting](#trim-insignificant-variants-for-faster-plotting)
+    - [Genome build conversion (liftover)](#genome-build-conversion-liftover)
+    - [Nearest-gene annotation for GWAS lead SNPs](#nearest-gene-annotation-for-gwas-lead-snps)
+3. [Application](#application)
+4. [Tip](#tip)
+5. [Installation](#installation)
+    - [From PyPI](#from-pypi)
+    - [From GitHub](#from-github)
+    - [Python virtual environment](#python-virtual-environment)
+6. [Test the installation](#test-the-installation)
+7. [Dependencies](#dependencies)
+8. [Command-line usage](#command-line-usage)
+    - [Linear Manhattan (default)](#linear-manhattan-default)
+    - [Circular Manhattan](#circular-manhattan)
+    - [Key options](#key-options)
+9. [Python API](#python-api)
+10. [Contributing](#contributing)
+11. [Contributors](#contributors)
+
+
+---------------------------------------------
+
+
+## Overview 
+
 This package will take any number of per SNP/variant summary statistics, be it GWAS, 
 selection scans (e.g. iHS, EHH, FST), etc and generate Manhattan plots. If given a single
 file, a single one-track Manhattan plot will be generated. Multiple files will result in 
@@ -29,8 +69,8 @@ option of the package should be used to indicate the column and then the package
 postions in hg19 to hg38 ensuring that hits table generation and plotting are done with one unified 
 corrdinate system.
 
-# Key features
-## Column auto-detection
+## Key features
+### Column auto-detection
 A key functionality of the package is its ability to auto-detect certain columns if ommited on the 
 command-line or python API:
 - Chromosome column: `-chr, --chrom_column` or ommited
@@ -53,7 +93,7 @@ bld_candidates = [build, 'BUILD', 'Genome', 'Genome_Build', 'Genome-build']
 
 > NB: Upper and lower cases of the candidates are also considered, making each candidate expanded 3 times.
 
-## Density-aware sub-sampling
+### Density-aware sub-sampling
 Another key feature is density-aware sub-sampling for Manhattan-style scatter plots.
 This was inspired by ``gwaslab``'s default behaviour (https://cloufield.github.io/gwaslab/). 
 
@@ -64,14 +104,14 @@ scan with the defaults below, this typically cuts the plotted point count from 1
 to ~200 K + a few hundred peaks — visually indistinguishable above the suggestive 
 band, but two orders of magnitude faster to render.
 
-## Trim insignificant variants for faster plotting
+### Trim insignificant variants for faster plotting
 An optional parameter `-tp, --trim_pval` is provided to increase speed even further. 
 Set with a value to exclude variants with p-value above a certain threshold, 
 e.g. `0.01 (1e-2)` or `0.001 (1e-3)`. Performed on top of the default auto-thin 
 feature above, it siginificant increases speed and reduces peak memory usage. 
 See benchmark figure (manuscript in preparation).
 
-## Genome build conversion (liftover)
+### Genome build conversion (liftover)
 Conversion of a both hg18 and hg19 positions to their hg38 equivalent is included through
 `pyliftover.LiftOver`.
 
@@ -81,7 +121,7 @@ column to specify the genome build of each position ('hg18', 'hg19', or 'hg38')
 using one coordinate system. If only 'hg18' or 'hg19' positions are present, no liftover 
 be necessary. Hence, liftover is only performed in cases of mixed genome builds.
 
-## Nearest-gene annotation for GWAS lead SNPs
+### Nearest-gene annotation for GWAS lead SNPs
 The package bundles GFF3 files in hg19 and hg38 coordinates processed to reduce size 
 for gene annotation. Also included are UCSC chain files for coordinate conversion (liftover).
   - ``chain_hg19_hg38`` -- UCSC LiftOver chain file for hg19 to hg38
@@ -100,12 +140,12 @@ for gene annotation. Also included are UCSC chain files for coordinate conversio
     ``Homo_sapiens.GRCh37.geneinfo.tsv.gz``.
 
 
-# Application
+## Application
 A potential useful application is **comparative visualization** of results from multiple imputation panels, 
 multiple populations, or multiple traits to observe shared genetic architecture.
 
 
-# Tip
+## Tip
 
 For signed non-pvalue statistics such as iHS, use `--signif_threshold` and 
 `--suggest_threshold` to specify lines to draw for iHS cutoff above and below zero, 
@@ -114,7 +154,7 @@ that is in the positive and negative axes.
 
 Read more in the package documentation page: https://pycmplot.readthedocs.io/en/latest/
 
----
+----------------------------
 
 ## Installation
 
@@ -141,24 +181,25 @@ pip install -e . --break-system-packages
 ```
 
 
-### Use python virtual environment if local installation is not possible
-```bash
-python -m venv ~/bin/pycmplot
+### Python virtual environment
 
-source ~/bin/pycmplot/bin/activate
+Use python virtual environment if local installation is not possible
 
-pip install --upgrade pip setuptools wheel
+```bash
+python -m venv ~/envs/pycmplot
+source ~/envs/pycmplot/bin/activate
 
-# then follow any of the installation steps above
+pip install --upgrade pip setuptools wheel
+pip install pycmplot
 ```
 
 
-# Test the installation
+## Test the installation
 ```bash
 pycmplot -h
 ```
 
-### Dependencies
+## Dependencies
 
 | Package | Purpose |
 |---------|---------|

pycmplot-0.3.1/benchmark/build_composite_figure.py

@@ -0,0 +1,199 @@
+#!/usr/bin/env python3
+"""Build the composite scaling figure used in the manuscript.
+
+Output: ``benchmark_composite_scaling.png`` (and an accompanying PDF), written
+to the directory passed via ``--outdir`` (default: same directory as this
+script).
+
+Layout (2 rows x 3 columns):
+
+  Top row    -- single-track wall-time scaling at 500K-10M variants:
+    (A) Manhattan
+    (B) Circular Manhattan
+    (C) QQ
+
+  Bottom row -- multi-track wall-time scaling at 1M and 2M variants
+                (multi-track benchmarks were only collected at 1M / 2M):
+    (D) Multi-track Manhattan          (pycmplot vs CMplot)
+    (E) Multi-track circular Manhattan (pycmplot vs CMplot)
+    (F) Shared legend
+
+The figure reuses :data:`collect_results.SERIES_STYLE` so styling stays
+consistent with the per-plot-type PDFs produced by
+``collect_results.py --plot``.
+
+Usage
+-----
+::
+
+    cd benchmark
+    python collect_results.py --resultsdir results --out results/summary.csv
+    python build_composite_figure.py                      # writes alongside this script
+    python build_composite_figure.py --outdir ../figures  # custom output dir
+    python build_composite_figure.py --summary path/to/summary.csv
+"""
+from __future__ import annotations
+
+import argparse
+import os
+import sys
+from pathlib import Path
+
+import matplotlib
+matplotlib.use("Agg")
+import matplotlib.pyplot as plt
+import pandas as pd
+
+# Resolve ``collect_results`` relative to this script so the figure builder
+# works regardless of the current working directory.
+SCRIPT_DIR = Path(__file__).resolve().parent
+sys.path.insert(0, str(SCRIPT_DIR))
+
+from collect_results import SERIES_STYLE, SIZE_N  # noqa: E402
+
+
+PANELS = [
+    # (row, col, letter, plot_type, title)
+    (0, 0, "A", "manhattan",            "Manhattan plot"),
+    (0, 1, "B", "circular",             "Circular Manhattan plot"),
+    (0, 2, "C", "qq",                   "QQ plot"),
+    (1, 0, "D", "multitrack_manhattan", "Multi-track Manhattan plot"),
+    (1, 1, "E", "multitrack_circular",  "Multi-track circular Manhattan plot"),
+]
+
+
+def build(summary_path: Path, outdir: Path, basename: str = "benchmark_composite_scaling") -> Path:
+    """Render the composite figure and return the path to the PNG output."""
+    summary = pd.read_csv(summary_path)
+
+    #fig, axes = plt.subplots(2, 3, figsize=(13, 7.5))
+    fig, axes = plt.subplots(2, 3, figsize=(6, 3.5))
+    plt.subplots_adjust(
+        top=0.94, bottom=0.07, left=0.06, right=0.98, wspace=0.30, hspace=0.45,
+    )
+
+    all_handles: list = []
+    all_labels: list = []
+    seen: set = set()
+
+    for r, c, letter, pt, title in PANELS:
+        ax = axes[r, c]
+        sub = summary[summary["plot_type"] == pt].copy()
+        sub["n_approx"] = sub["size_label"].map(SIZE_N)
+        sub = sub.dropna(subset=["n_approx"])
+
+        tools_in_data = list(sub["tool"].unique())
+        ordered_tools = (
+            [t for t in SERIES_STYLE if t in tools_in_data]
+            + [t for t in tools_in_data if t not in SERIES_STYLE]
+        )
+
+        for tool in ordered_tools:
+            tdf = sub[sub["tool"] == tool].sort_values("n_approx")
+            if tdf.empty:
+                continue
+            s = SERIES_STYLE.get(
+                tool, dict(label=tool, color="#888780", ls="-", marker="o"),
+            )
+            line, = ax.plot(
+                tdf["n_approx"], tdf["wall_time_mean"],
+                marker=s["marker"], linestyle=s["ls"], color=s["color"],
+                label=s["label"] or tool,
+                linewidth=1, markersize=2,
+            )
+            ax.fill_between(
+                tdf["n_approx"],
+                tdf["wall_time_mean"] - tdf["wall_time_sd"].fillna(0),
+                tdf["wall_time_mean"] + tdf["wall_time_sd"].fillna(0),
+                alpha=0.12, color=s["color"], linewidth=0,
+            )
+            label = s["label"] or tool
+            if label not in seen:
+                all_handles.append(line)
+                all_labels.append(label)
+                seen.add(label)
+
+        ax.set_xscale("log")
+        ax.set_yscale("log")
+        ax.set_xlabel("Number of variants", fontsize=7) #fontsize=10
+        if c == 0:
+            ax.set_ylabel("Wall-clock time (s)", fontsize=7) #fontsize=10
+        ax.set_title(f"({letter}) {title}", fontsize=7, loc="left") #fontsize=10
+        ax.grid(True, which="both", linestyle="--", linewidth=0.3, alpha=0.5)
+        ax.tick_params(labelsize=5)
+
+    # Bottom-right cell (1, 2) holds the shared legend so each axes stays
+    # uncluttered.
+    legend_ax = axes[1, 2]
+    legend_ax.axis("off")
+    legend_ax.legend(
+        all_handles, all_labels,
+        loc="center", ncol=1, fontsize=5, frameon=False,
+        title="Tool", title_fontsize=5,
+    )
+
+    outdir.mkdir(parents=True, exist_ok=True)
+    png_path = outdir / f"{basename}.png"
+    pdf_path = outdir / f"{basename}.pdf"
+    tif_path = outdir / f"{basename}.TIF"
+    #eps_path = outdir / f"{basename}.eps"
+    fig.savefig(png_path, dpi=300, bbox_inches="tight")
+    fig.savefig(tif_path, dpi=300, bbox_inches="tight")
+    #fig.savefig(eps_path, dpi=300, bbox_inches="tight")
+    fig.savefig(pdf_path, bbox_inches="tight")
+    plt.close(fig)
+
+    print(f"Wrote {png_path}")
+    print(f"Wrote {tif_path}")
+    #print(f"Wrote {eps_path}")
+    print(f"Wrote {pdf_path}")
+    return png_path
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description="Build the composite scaling figure for the manuscript.",
+    )
+    parser.add_argument(
+        "--summary",
+        type=Path,
+        default=None,
+        help=(
+            "Path to summary.csv produced by collect_results.py.  "
+            "Default: <script_dir>/summary.csv, then <script_dir>/results/summary.csv."
+        ),
+    )
+    parser.add_argument(
+        "--outdir",
+        type=Path,
+        default=SCRIPT_DIR,
+        help="Output directory for the figure files (default: this script's directory).",
+    )
+    parser.add_argument(
+        "--basename",
+        type=str,
+        default="benchmark_composite_scaling",
+        help="Output file basename (without extension).  Default: benchmark_composite_scaling.",
+    )
+    args = parser.parse_args()
+
+    if args.summary is None:
+        candidates = [SCRIPT_DIR / "summary.csv", SCRIPT_DIR / "results" / "summary.csv"]
+        for c in candidates:
+            if c.exists():
+                args.summary = c
+                break
+        else:
+            sys.exit(
+                "Could not locate summary.csv.  Pass --summary or run "
+                "`python collect_results.py --resultsdir results --out results/summary.csv` first."
+            )
+
+    if not args.summary.exists():
+        sys.exit(f"summary file not found: {args.summary}")
+
+    build(args.summary, args.outdir, basename=args.basename)
+
+
+if __name__ == "__main__":
+    main()

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/__init__.py

@@ -47,4 +47,4 @@ __all__ = [
     "ResourceConfig",
 ]
 
-__version__ = "0.2.9"
+__version__ = "0.3.1"

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/_core.py

@@ -281,6 +281,7 @@ def main() -> None:
             highlight_color = highlight_color,
             highlight_line = highlight_line,
             highlight_line_color = highlight_line_color,
+            suggest_line = True if suggest_threshold is not None else False,
             colors = colors,
             point_size=point_size,
             chrom_label_side = chrom_label_side,
@@ -318,6 +319,8 @@ def main() -> None:
             highlight_color=highlight_color,
             highlight_line=highlight_line,
             highlight_line_color=highlight_line_color,
+            signif_line = signif_line,
+            suggest_line = True if suggest_threshold is not None else False,
             annotate=annotate,
             annotation_size=annotation_size,
             hits_table=hits_table if not hits_table.empty else None,
@@ -351,7 +354,7 @@ def main() -> None:
                 max_points=qq_max_points,                
                 output_path=qq_stem,
                 colors=colors,
-                signif_threshold=signif_threshold or 5e-8,
+                signif_threshold=signif_threshold,
                 dpi=dpi,
                 fontsize=fsize,
                 fig_format=output_format,
@@ -363,7 +366,7 @@ def main() -> None:
                 thin_below=thin_below,
                 max_points=qq_max_points,                
                 colors=colors,
-                signif_threshold=signif_threshold or 5e-8,
+                signif_threshold=signif_threshold,
                 dpi=dpi,
                 fontsize=fsize,
                 title=plot_title,
@@ -378,7 +381,7 @@ def main() -> None:
                 max_points=qq_max_points,
                 colors=colors,
                 ncols=qq_ncols,
-                signif_threshold=signif_threshold or 5e-8,
+                signif_threshold=signif_threshold,
                 dpi=dpi,
                 fontsize=fsize,
                 title=plot_title,

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/annotation.py

@@ -589,11 +589,11 @@ def get_annotation_column(
                     try:
                         if row["genic"]:
                             label_clm = "nearest_upstream_gene"
-                            label_msg = "'POS' is genic"
+                            label_msg = f"Signal {row['SNP']} at {row['POS']} is genic [{row['nearest_upstream_gene']}]"
                         else:
                             label_clm = "top_gene"
                             label_msg = "'POS' is not genic"
-                        logger.info("%s", label_msg)
+                        #logger.info("%s", label_msg)
                     except Exception:
                         logger.warning(
                             "Annotation columns '%s' and '%s' not found in hits table: %s; "

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/cli.py

@@ -365,13 +365,15 @@ def get_arguments(descmsg: str = DESCMSG) -> argparse.Namespace:
     )
     opt.add_argument(
         "-sig", "--signif_threshold",
-        default=None, const=5e-8, nargs="?", type=float, metavar="float",
-        help="Genome-wide significance threshold (default: 5e-8)."
+        default=None, const=None, 
+        nargs="?", type=float, metavar="float",
+        help="Genome-wide significance threshold (default: 0.05/number of records)."
     )
     opt.add_argument(
         "-sigl", "--signif_line",
-        default=None, const=5e-8, nargs="?", type=float, metavar="float",
-        help="Value for genome-wide significance line if different from `-sig` (default: 5e-8)."
+        default=None, const=999999, # arbitriary number to evaluate
+        nargs="?", type=float, metavar="float",
+        help="Value for genome-wide significance line if different from `-sig` (default: 0.05/number of records)."
     )
     opt.add_argument(
         "-sug", "--suggest_threshold",
@@ -403,8 +405,8 @@ def get_arguments(descmsg: str = DESCMSG) -> argparse.Namespace:
         help="Highlight significant loci."
     )
     opt.add_argument(
-        "-ht", "--highlight_thresh", default=5e-8, type=float, metavar="float",
-        help="P-value threshold for highlighting (default: 5e-8)."
+        "-ht", "--highlight_thresh", default=None, type=float, metavar="float",
+        help="P-value threshold for highlighting (default: '--signif_threshold')."
     )
     opt.add_argument(
         "-hc", "--highlight_color", default="brown", type=str, metavar="str",

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/io.py

@@ -888,9 +888,9 @@ def get_sumstats_and_merged_sector_list(
     table_out: Optional[str] = None,
     signif_threshold: Optional[float] = None,
     signif_line: Optional[float] = None,
-    suggest_threshold: Optional[float] = None,
+    suggest_threshold: Optional[float] = 1e-5,
     highlight: Optional[bool] = False,
-    highlight_thresh: Optional[float] = 5e-08,
+    highlight_thresh: Optional[float] = None,
     resources: Optional[ResourceConfig] = None,
     compute_pvals: bool = True,
     auto_thin: bool = True,
@@ -1017,6 +1017,8 @@ def get_sumstats_and_merged_sector_list(
 
     sumstats_loaded: dict[str, list] = {}
     pval_dict: dict[str, np.ndarray | pd.Series] = {}
+    snp_counts: dict[str, np.ndarray | pd.Series] = {}
+    signif_lines: list[dict[str, float]] = []
     all_lead_snps: list[pd.DataFrame] = []
 
     for label in sumstats.keys() & (file_info or {}).keys():
@@ -1078,6 +1080,40 @@ def get_sumstats_and_merged_sector_list(
         else:
             pval_dict[label] = None
 
+        # Get SNP counts for significance threshold calculation
+        snp_counts[label] = len(df["P"].dropna().astype(float).values)
+        
+        # Derive significance/suggestive thresholds
+        n = snp_counts[label]
+        if signif_threshold is None:
+            #last_label = list(sumstats_loaded)[-1]
+            signif_threshold = max(0.05 / n, 5e-8)
+
+        if suggest_threshold is not None:
+            suggest_line = suggest_threshold
+        else:
+            suggest_line = 1e-5
+        if logp:
+            suggest_line = -np.log10(suggest_line)
+
+        if signif_line is None:
+            signif_line = signif_threshold
+            if logp:
+                signif_line = -np.log10(signif_line)
+        else:
+            # significance line was set without value
+            # fallback to sig_thresh
+            if signif_line == 999999:
+                signif_line = signif_threshold
+            # significance line was set with value, use value
+            else:
+                signif_line = np.float64(signif_line)
+
+            if logp and signif_line < 1:
+                signif_line = -np.log10(signif_line)
+
+        signif_lines.append({"genome": signif_line, "suggestive": suggest_line})
+
         # Density-aware auto-thinning for Manhattan / circular rendering.
         # Applied after lead-SNP extraction so the leads come from the full
         # dataset, and after liftover so coordinates are final.  Variants
@@ -1189,11 +1225,12 @@ def get_sumstats_and_merged_sector_list(
         # into ``sumstats_loaded[label][0]`` here raised ``KeyError`` (e.g.
         # ``KeyError: 'MCV'``) the first time the liftover branch fired on
         # a given track.
+        builds = df["BUILD"].unique()
         if "BUILD" in df.columns and (
-            "hg19" in df["BUILD"].unique() or "hg18" in df["BUILD"].unique()
+            "hg18" in builds or ("hg19" in builds and "hg38" in builds)
         ):
             builds_present = sorted(
-                b for b in df["BUILD"].unique() if b in {"hg18", "hg19"}
+                b for b in builds if b in {"hg18", "hg19"}
             )
             logger.info(
                 "Converting %s coordinates to hg38 ...", "/".join(builds_present)
@@ -1210,7 +1247,7 @@ def get_sumstats_and_merged_sector_list(
             df=df,
             window=500_000,
             highlight=highlight,
-            highlight_thresh=highlight_thresh,
+            highlight_thresh=highlight_thresh if highlight_thresh is not None else signif_threshold,
             logp=logp,
         )
 
@@ -1222,6 +1259,9 @@ def get_sumstats_and_merged_sector_list(
         #    logp=logp,
         #)
 
+        if not leads.empty:
+            leads = leads[leads["P"] <= signif_threshold]
+
         all_lead_snps.append(leads)
 
         # Number of distinct chromosomes (for track sorting)
@@ -1234,11 +1274,7 @@ def get_sumstats_and_merged_sector_list(
         if all_lead_snps
         else pd.DataFrame()
     )
-    if not all_lead_snps_df.empty and signif_threshold:
-        all_lead_snps_df = all_lead_snps_df[
-            all_lead_snps_df["P"] <= signif_threshold
-        ]
-
+  
     hits_table = (
         get_hits_summary_table(
             leads_df=all_lead_snps_df,
@@ -1250,37 +1286,6 @@ def get_sumstats_and_merged_sector_list(
         else pd.DataFrame()
     )
 
-    # Derive significance/suggestive thresholds
-    if not signif_threshold:
-        if trim_pval:
-            signif_threshold = 5e-8
-        elif sumstats_loaded:
-            last_label = list(sumstats_loaded)[-1]
-            n = len(sumstats_loaded[last_label][0]["P"])
-            signif_threshold = max(0.05 / n, 5e-8)
-        else:
-            signif_threshold = 5e-8
-
-    if not suggest_threshold:
-        suggest_threshold = 1e-5
-
-    suggest_line = suggest_threshold
-    if logp:
-        suggest_line = -np.log10(suggest_threshold)
-
-    if signif_line is None:
-        signif_line = signif_threshold
-        if logp:
-            signif_line = -np.log10(signif_threshold)
-    else:
-        if logp and signif_line < 1:
-            signif_line = -np.log10(signif_line)
-
-    signif_lines = [
-        {"genome": signif_line, "suggestive": suggest_line}
-        for _ in sumstats
-    ]
-
     # sort dicts by user-supplied order
     sumstats_loaded = {key: sumstats_loaded[key] for key in labels if key in sumstats_loaded}
     pval_dict = {key: pval_dict[key] for key in labels if key in pval_dict}

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/plotting/circular.py

@@ -131,10 +131,10 @@ def plot_circosm(
     track_index: int = 0,
     assoc_label: Optional[str] = None,
     logp: bool = True,
-    signif_line: Optional[float] = 5e-8,
-    signif_threshold: Optional[float] = 5e-8,
-    suggest_line: Optional[float] = 1e-5,
-    suggest_threshold: Optional[float] = 1e-5,
+    signif_line: Optional[float] = None,
+    signif_threshold: Optional[float] = None,
+    suggest_line: bool = False,
+    suggest_threshold: Optional[float] = None,
     highlight: bool = False,
     highlight_color: str = 'brown',
     colors: Optional[list[str]] = ['steelblue','orange'],
@@ -336,7 +336,7 @@ def plot_circosm(
     # ------------------------------------------------------------------
     # Significance lines
     # ------------------------------------------------------------------
-    if signif_line:
+    if signif_line is not None:
         track.line(
             x=[sector.start, sector.end],
             y=[genome_wide_sig, genome_wide_sig],
@@ -365,12 +365,13 @@ def plot_circular(
     label_col: str = None,
     chrom_label_side: str = 'inside',
     chrom_label_size: float = 6,
-    signif_line: float = 5e-8,
+    signif_line: float = None,
     highlight: bool = False,
-    highlight_thresh: float = 5e-8,
+    highlight_thresh: float = None,
     highlight_color: str = 'brown',
     highlight_line: bool = False,
     highlight_line_color: str = 'grey',
+    suggest_line: bool = False,
     colors: list[str] = ['steelblue','silver'],
     point_size: float = 6,
     track_label_size: float = 6,
@@ -557,6 +558,7 @@ def plot_circular(
 
     chrom_label_loc = outside_loc if chrom_label_side == "outside" else inside_loc
 
+    """
     if not signif_lines:
         signif_line = -np.log10(signif_line) if signif_line < 1 else signif_line
         suggest_line = -np.log10(1e-5)
@@ -564,6 +566,7 @@ def plot_circular(
             {"genome": signif_line, "suggestive": suggest_line}
             for _ in sumstats_loaded
         ]      
+    """
 
     for index, (sector_radius, sumstats_key, sumstats_value, signif_dict) in enumerate(
         zip(
@@ -607,9 +610,9 @@ def plot_circular(
                 assoc_by_chr=assoc_by_chr,
                 assoc_label=sumstat_name,
                 logp=logp,
-                signif_line=sig_thresh,
+                signif_line=signif_line,
                 signif_threshold=sig_thresh,
-                suggest_line=True if signif_line else False,
+                suggest_line=suggest_line,
                 suggest_threshold=sug_thresh,
                 highlight=highlight,
                 highlight_color=highlight_color,

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot/plotting/linear.py

@@ -960,6 +960,9 @@ def plot_linearm(
     highlight_color: str = 'brown',
     highlight_line: bool = False,
     highlight_line_color: str = 'grey',
+    signif_line: Optional[float] = None,
+    suggest_line: bool = False,
+    sig_lines: Optional[list[dict]] = None,
     logp: bool = True,
     label_col: Optional[str] = 'SNP',
     chr_order: Optional[list[str]] = None,
@@ -969,7 +972,6 @@ def plot_linearm(
     annot_rail_frac: float = 0.95,
     point_size: float = 8,
     colors: Optional[list[str]] = ['steelblue','silver'],
-    sig_lines: Optional[list[dict]] = None,
     plt_name: Optional[str] = None,
     no_track_labels: bool = False,
     ylabel: Optional[str] = None,
@@ -1355,10 +1357,12 @@ def plot_linearm(
 
         if sig_lines is not None and i < len(sig_lines):
             sl = sig_lines[i]
-            if "genome" in sl:
-                ax.axhline(y=sl["genome"], color="orangered", linestyle="--", linewidth=0.5)
-            if "suggestive" in sl:
-                ax.axhline(y=sl["suggestive"], color="navy", linestyle="--", linewidth=0.5)
+            if signif_line is not None:
+                    if "genome" in sl:
+                        ax.axhline(y=sl["genome"], color="orangered", linestyle="--", linewidth=0.5)
+            if suggest_line:
+                if "suggestive" in sl:
+                    ax.axhline(y=sl["suggestive"], color="navy", linestyle="--", linewidth=0.5)
 
         ax.spines[["top", "right"]].set_visible(False)
 
@@ -1375,7 +1379,6 @@ def plot_linearm(
             differences = np.diff(df_chr['POS']).tolist()
             less_than_spread_width.append(list(filter(lambda x: x < s_width, differences)))
             less_than_spread_width = [l for l in less_than_spread_width if not len(l) == 0]
-        print(len(less_than_spread_width))
         if len(less_than_spread_width) < 5:
             _draw_annotation_arrows(
                 ax_annot,
@@ -1484,7 +1487,10 @@ def plot_linear(
     highlight: bool = False,
     highlight_color: str = 'brown',
     highlight_line: bool = False,
-    highlight_line_color: str = 'grey',    
+    highlight_line_color: str = 'grey',
+    signif_lines: Optional[dict] = None,
+    signif_line: Optional[float] = None,
+    suggest_line: bool = False,
     hits_table: Optional[pd.DataFrame] = None,
     annotate: str = None,
     annotation_size: float = 8,
@@ -1493,7 +1499,6 @@ def plot_linear(
     linear_track_spacing: Optional[float] = None,
     annot_rail_frac: Optional[float] = 0.98,
     colors: list[str] = ['steelblue','silver'],
-    signif_lines: Optional[dict] = None,
     plot_title: Optional[str] = None,
     no_track_labels: bool = False,
     ylabel: Optional[str] = None,
@@ -1638,6 +1643,8 @@ def plot_linear(
         highlight_color = highlight_color,
         highlight_line = highlight_line,
         highlight_line_color = highlight_line_color,
+        signif_line = signif_line,
+        suggest_line = suggest_line,        
         annotate=annotate,
         annotation_size=annotation_size,      
         annot_df=hits_table if hits_table is not None and not hits_table.empty else None,

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pycmplot
-Version: 0.2.9
+Version: 0.3.1
 Summary: Multi-track circular and linear Manhattan plot generation for GWAS summary statistics
 Author: Kevin Esoh
 Author-email: Kevin Esoh <kesohku1@jh.edu>
@@ -39,16 +39,56 @@ Dynamic: license-file
 
 # pycmplot
 
-Multi-track **circular** and **linear** Manhattan plot generation for GWAS summary statistics.
+<div>
+  <h1 align="center">Multi-track circular and linear Manhattan plotting in Python.</h1>
+</div>
+
+<p align="center">
+  <img width="600" height="400" src="docs/pycmplot-logo-circular.png">
+</p>
+
 
 ```
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
-|  PACKAGE FOR CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
-|                    Kevin Esoh, 2026                  |
-|                    kesohku1@jh.edu                   |
-#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+                    |  MULTI-TRACK CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
+                    |                      in Python                       |
+                    |                    Kevin Esoh, 2026                  |
+                    |                    kesohku1@jh.edu                   |
+                    #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 ```
 
+----------------------------------------------
+
+## Content
+1. [Overview](#overview)
+2. [Key features](#key-features)
+    - [Column auto-detection](#column-auto-detection)
+    - [Density-aware sub-sampling](#density-aware-sub-sampling)
+    - [Trim insignificant variants for faster plotting](#trim-insignificant-variants-for-faster-plotting)
+    - [Genome build conversion (liftover)](#genome-build-conversion-liftover)
+    - [Nearest-gene annotation for GWAS lead SNPs](#nearest-gene-annotation-for-gwas-lead-snps)
+3. [Application](#application)
+4. [Tip](#tip)
+5. [Installation](#installation)
+    - [From PyPI](#from-pypi)
+    - [From GitHub](#from-github)
+    - [Python virtual environment](#python-virtual-environment)
+6. [Test the installation](#test-the-installation)
+7. [Dependencies](#dependencies)
+8. [Command-line usage](#command-line-usage)
+    - [Linear Manhattan (default)](#linear-manhattan-default)
+    - [Circular Manhattan](#circular-manhattan)
+    - [Key options](#key-options)
+9. [Python API](#python-api)
+10. [Contributing](#contributing)
+11. [Contributors](#contributors)
+
+
+---------------------------------------------
+
+
+## Overview 
+
 This package will take any number of per SNP/variant summary statistics, be it GWAS, 
 selection scans (e.g. iHS, EHH, FST), etc and generate Manhattan plots. If given a single
 file, a single one-track Manhattan plot will be generated. Multiple files will result in 
@@ -68,8 +108,8 @@ option of the package should be used to indicate the column and then the package
 postions in hg19 to hg38 ensuring that hits table generation and plotting are done with one unified 
 corrdinate system.
 
-# Key features
-## Column auto-detection
+## Key features
+### Column auto-detection
 A key functionality of the package is its ability to auto-detect certain columns if ommited on the 
 command-line or python API:
 - Chromosome column: `-chr, --chrom_column` or ommited
@@ -92,7 +132,7 @@ bld_candidates = [build, 'BUILD', 'Genome', 'Genome_Build', 'Genome-build']
 
 > NB: Upper and lower cases of the candidates are also considered, making each candidate expanded 3 times.
 
-## Density-aware sub-sampling
+### Density-aware sub-sampling
 Another key feature is density-aware sub-sampling for Manhattan-style scatter plots.
 This was inspired by ``gwaslab``'s default behaviour (https://cloufield.github.io/gwaslab/). 
 
@@ -103,14 +143,14 @@ scan with the defaults below, this typically cuts the plotted point count from 1
 to ~200 K + a few hundred peaks — visually indistinguishable above the suggestive 
 band, but two orders of magnitude faster to render.
 
-## Trim insignificant variants for faster plotting
+### Trim insignificant variants for faster plotting
 An optional parameter `-tp, --trim_pval` is provided to increase speed even further. 
 Set with a value to exclude variants with p-value above a certain threshold, 
 e.g. `0.01 (1e-2)` or `0.001 (1e-3)`. Performed on top of the default auto-thin 
 feature above, it siginificant increases speed and reduces peak memory usage. 
 See benchmark figure (manuscript in preparation).
 
-## Genome build conversion (liftover)
+### Genome build conversion (liftover)
 Conversion of a both hg18 and hg19 positions to their hg38 equivalent is included through
 `pyliftover.LiftOver`.
 
@@ -120,7 +160,7 @@ column to specify the genome build of each position ('hg18', 'hg19', or 'hg38')
 using one coordinate system. If only 'hg18' or 'hg19' positions are present, no liftover 
 be necessary. Hence, liftover is only performed in cases of mixed genome builds.
 
-## Nearest-gene annotation for GWAS lead SNPs
+### Nearest-gene annotation for GWAS lead SNPs
 The package bundles GFF3 files in hg19 and hg38 coordinates processed to reduce size 
 for gene annotation. Also included are UCSC chain files for coordinate conversion (liftover).
   - ``chain_hg19_hg38`` -- UCSC LiftOver chain file for hg19 to hg38
@@ -139,12 +179,12 @@ for gene annotation. Also included are UCSC chain files for coordinate conversio
     ``Homo_sapiens.GRCh37.geneinfo.tsv.gz``.
 
 
-# Application
+## Application
 A potential useful application is **comparative visualization** of results from multiple imputation panels, 
 multiple populations, or multiple traits to observe shared genetic architecture.
 
 
-# Tip
+## Tip
 
 For signed non-pvalue statistics such as iHS, use `--signif_threshold` and 
 `--suggest_threshold` to specify lines to draw for iHS cutoff above and below zero, 
@@ -153,7 +193,7 @@ that is in the positive and negative axes.
 
 Read more in the package documentation page: https://pycmplot.readthedocs.io/en/latest/
 
----
+----------------------------
 
 ## Installation
 
@@ -180,24 +220,25 @@ pip install -e . --break-system-packages
 ```
 
 
-### Use python virtual environment if local installation is not possible
-```bash
-python -m venv ~/bin/pycmplot
+### Python virtual environment
 
-source ~/bin/pycmplot/bin/activate
+Use python virtual environment if local installation is not possible
 
-pip install --upgrade pip setuptools wheel
+```bash
+python -m venv ~/envs/pycmplot
+source ~/envs/pycmplot/bin/activate
 
-# then follow any of the installation steps above
+pip install --upgrade pip setuptools wheel
+pip install pycmplot
 ```
 
 
-# Test the installation
+## Test the installation
 ```bash
 pycmplot -h
 ```
 
-### Dependencies
+## Dependencies
 
 | Package | Purpose |
 |---------|---------|

{pycmplot-0.2.9 → pycmplot-0.3.1}/pycmplot.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 setup.cfg
 setup.py
 benchmark/bench_python.py
+benchmark/build_composite_figure.py
 benchmark/collect_results.py
 benchmark/generate_multi_sumstats.py
 benchmark/generate_sumstats.py

{pycmplot-0.2.9 → pycmplot-0.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pycmplot"
-version = "0.2.9"
+version = "0.3.1"
 description = "Multi-track circular and linear Manhattan plot generation for GWAS summary statistics"
 readme = "README.md"
 license = "MIT"

{pycmplot-0.2.9 → pycmplot-0.3.1}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pycmplot
-version = 0.2.9
+version = 0.3.1
 author = Kevin Esoh
 author_email = kesohku1@jh.edu
 description = Multi-track circular and linear Manhattan plot generation for GWAS summary statistics