pycmplot 0.1.0__tar.gz

pycmplot-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Kevin Esoh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pycmplot-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pycmplot
+Version: 0.1.0
+Summary: Multi-track circular and linear Manhattan plot generation for GWAS summary statistics
+Author: Kevin Esoh
+Author-email: Kevin Esoh <kesohku1@jhmi.edu>
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.5
+Requires-Dist: numpy>=1.23
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: pillow>=9.0
+Requires-Dist: pycirclize>=0.6
+Requires-Dist: natsort>=8.0
+Requires-Dist: adjustText>=0.8
+Requires-Dist: pyliftover>=0.4
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Dynamic: license-file
+
+# pycmplot
+
+Multi-track **circular** and **linear** Manhattan plot generation for GWAS summary statistics.
+
+```
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+|  PACKAGE FOR CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
+|                    Kevin Esoh, 2026                  |
+|                    kesohku1@jh.edu                   |
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+```
+
+---
+
+## Installation
+
+### From PyPI
+```bash
+pip install pycmplot
+```
+
+
+### From source code
+```bash
+wget <url>
+
+tar zxvf ...
+
+cd pycmplot-xxx
+
+pip install -e .
+```
+
+
+### From GitHub
+```bash
+git clone https://github.com/esohkevin/pycmplot.git
+
+cd pycmplot
+
+pip install -e .
+
+# or
+
+pip install -e . --break-system-packages
+```
+
+
+### Use python virtual environment if local installation is not possible
+```bash
+python -m venv ~/bin/pycmplot
+
+source ~/bin/pycmplot/bin/activate
+
+pip install --upgrade pip setuptools wheel
+
+# then follow any of the installation steps above
+```
+
+
+# Test the installation
+```bash
+pycmplot -h
+```
+
+### Dependencies
+
+| Package | Purpose |
+|---------|---------|
+| pandas, numpy | Data loading & statistics |
+| matplotlib | Plotting backend |
+| pycirclize | Circular (Circos-style) tracks |
+| natsort | Natural chromosome sorting |
+| adjustText | Label collision avoidance |
+| pyliftover | hg19 to hg38 coordinate conversion |
+| Pillow | Image utilities |
+
+---
+
+
+## Command-line usage
+
+### Linear Manhattan (default)
+
+```bash
+pycmplot \
+  --sum_stats HbF.tsv.gz,MCV.txt.gz,MCH.tsv.gz \
+  --labels HbF,MCV,MCH \
+  --logp \
+  --signif_line \
+  --highlight \
+  --annotate GENE \
+  --output_dir ./results \
+  --output_format png \
+  --dpi 300
+```
+
+### Circular Manhattan
+
+```bash
+pycmplot \
+  --sum_stats HbF.tsv.gz,MCV.tsv.gz \
+  --labels HbF,MCV \
+  --mode cm \
+  --logp \
+  --signif_threshold \
+  --plot_title "RBC Traits" \
+  --output_dir ./results
+```
+
+### Key options
+
+| Flag | Description | Default |
+|------|-------------|---------|
+| `-s, --sum_stats` | Comma-separated sumstats files | **required** |
+| `-l, --labels` | Comma-separated track labels | **required** |
+| `-m, --mode` | `lm` linear or `cm` circular | `lm` |
+| `-qq, --qq_plot` | Also generate a QQ-plot | off (coming soon...) |
+| `--logp` | Plot -log10(p) | off |
+| `-sig, --signif_threshold` | Genome-wide significance threshold | off (auto 0.05/N) |
+| `-sigl, --signif_line` | Value for genome-wide significance line if different from `-sig` | `-sig` |
+| `-sug, --suggest_threshold` | Suggestive significance line | off |
+| `-hl, --highlight` | Highlight significant loci | off |
+| `-a, --annotate` | Annotate with `SNP` or `GENE` | `SNP` |
+| `-tp, --trim_pval` | Trim variants above this p-value for speed | off |
+| `-st, --sort_track` | Sort tracks by `label` or `chrom_len` | input order |
+| `-od, --output_dir` | Output directory | `.` |
+| `-of, --output_format` | Output format (`png`, `pdf`, `svg`, `jpg`) | `png` |
+
+Run `pycmplot -h` for the full option list.
+
+---
+
+## Python API
+
+```python
+from pycmplot import plot_linear
+import pandas as pd
+
+df1 = pd.read_csv("HbF.tsv.gz", sep="\t")
+df2 = pd.read_csv("MCV.tsv.gz", sep="\t")
+
+plot_linear(
+    tracks=[df1, df2],
+    track_labels=["HbF", "MCV"],
+    chr_col="CHR",
+    pos_col="POS",
+    p_col="P",
+    logp=True,
+    highlight=True,
+    plot_title="results/HbF_MCV.png",
+    figsize=(15, 8),
+)
+```
+
+---
+
+_Under development_

pycmplot-0.1.0/README.md

@@ -0,0 +1,158 @@
+# pycmplot
+
+Multi-track **circular** and **linear** Manhattan plot generation for GWAS summary statistics.
+
+```
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+|  PACKAGE FOR CIRCULAR AND LINEAR MANHATTAN PLOTTING  |
+|                    Kevin Esoh, 2026                  |
+|                    kesohku1@jh.edu                   |
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
+```
+
+---
+
+## Installation
+
+### From PyPI
+```bash
+pip install pycmplot
+```
+
+
+### From source code
+```bash
+wget <url>
+
+tar zxvf ...
+
+cd pycmplot-xxx
+
+pip install -e .
+```
+
+
+### From GitHub
+```bash
+git clone https://github.com/esohkevin/pycmplot.git
+
+cd pycmplot
+
+pip install -e .
+
+# or
+
+pip install -e . --break-system-packages
+```
+
+
+### Use python virtual environment if local installation is not possible
+```bash
+python -m venv ~/bin/pycmplot
+
+source ~/bin/pycmplot/bin/activate
+
+pip install --upgrade pip setuptools wheel
+
+# then follow any of the installation steps above
+```
+
+
+# Test the installation
+```bash
+pycmplot -h
+```
+
+### Dependencies
+
+| Package | Purpose |
+|---------|---------|
+| pandas, numpy | Data loading & statistics |
+| matplotlib | Plotting backend |
+| pycirclize | Circular (Circos-style) tracks |
+| natsort | Natural chromosome sorting |
+| adjustText | Label collision avoidance |
+| pyliftover | hg19 to hg38 coordinate conversion |
+| Pillow | Image utilities |
+
+---
+
+
+## Command-line usage
+
+### Linear Manhattan (default)
+
+```bash
+pycmplot \
+  --sum_stats HbF.tsv.gz,MCV.txt.gz,MCH.tsv.gz \
+  --labels HbF,MCV,MCH \
+  --logp \
+  --signif_line \
+  --highlight \
+  --annotate GENE \
+  --output_dir ./results \
+  --output_format png \
+  --dpi 300
+```
+
+### Circular Manhattan
+
+```bash
+pycmplot \
+  --sum_stats HbF.tsv.gz,MCV.tsv.gz \
+  --labels HbF,MCV \
+  --mode cm \
+  --logp \
+  --signif_threshold \
+  --plot_title "RBC Traits" \
+  --output_dir ./results
+```
+
+### Key options
+
+| Flag | Description | Default |
+|------|-------------|---------|
+| `-s, --sum_stats` | Comma-separated sumstats files | **required** |
+| `-l, --labels` | Comma-separated track labels | **required** |
+| `-m, --mode` | `lm` linear or `cm` circular | `lm` |
+| `-qq, --qq_plot` | Also generate a QQ-plot | off (coming soon...) |
+| `--logp` | Plot -log10(p) | off |
+| `-sig, --signif_threshold` | Genome-wide significance threshold | off (auto 0.05/N) |
+| `-sigl, --signif_line` | Value for genome-wide significance line if different from `-sig` | `-sig` |
+| `-sug, --suggest_threshold` | Suggestive significance line | off |
+| `-hl, --highlight` | Highlight significant loci | off |
+| `-a, --annotate` | Annotate with `SNP` or `GENE` | `SNP` |
+| `-tp, --trim_pval` | Trim variants above this p-value for speed | off |
+| `-st, --sort_track` | Sort tracks by `label` or `chrom_len` | input order |
+| `-od, --output_dir` | Output directory | `.` |
+| `-of, --output_format` | Output format (`png`, `pdf`, `svg`, `jpg`) | `png` |
+
+Run `pycmplot -h` for the full option list.
+
+---
+
+## Python API
+
+```python
+from pycmplot import plot_linear
+import pandas as pd
+
+df1 = pd.read_csv("HbF.tsv.gz", sep="\t")
+df2 = pd.read_csv("MCV.tsv.gz", sep="\t")
+
+plot_linear(
+    tracks=[df1, df2],
+    track_labels=["HbF", "MCV"],
+    chr_col="CHR",
+    pos_col="POS",
+    p_col="P",
+    logp=True,
+    highlight=True,
+    plot_title="results/HbF_MCV.png",
+    figsize=(15, 8),
+)
+```
+
+---
+
+_Under development_

pycmplot-0.1.0/pycmplot/__init__.py

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+"""
+pycmplot
+========
+Multi-track circular and linear Manhattan plot generation for GWAS summary statistics.
+
+Quickstart
+----------
+Command-line::
+
+    pycmplot -s file1.gz,file2.gz -l HbF,MCV --logp --mode lm
+
+Python API::
+
+    from pycmplot.plotting import plot_linear, plot_circular
+    from pycmplot.stats import get_lead_snps
+    from pycmplot.annotation import get_hits_summary_table
+
+Public surface
+--------------
+"""
+
+from pycmplot.plotting.linear import plot_linear
+from pycmplot.plotting.circular import plot_circular, compute_track_radii_dict
+from pycmplot.stats import get_lead_snps, get_highlight_snps
+from pycmplot.io import get_sumstats_and_merged_sector_list
+from pycmplot.annotation import get_hits_summary_table
+from pycmplot.constants import hg38_chr_lengths, BIOTYPE_WEIGHTS
+from pycmplot.resources import ResourceConfig
+
+__all__ = [
+    "plot_linear",
+    "plot_circular",
+    "compute_track_radii_dict",
+    "get_lead_snps",
+    "get_highlight_snps",
+    "get_sumstats_and_merged_sector_list",
+    "get_hits_summary_table",
+    "hg38_chr_lengths",
+    "BIOTYPE_WEIGHTS",
+    "ResourceConfig",
+]
+
+__version__ = "0.1.0"