pycmplot

Getting Started

  • Installation
    • Requirements
    • From PyPI (recommended)
    • From GitHub (development version)
    • Using a virtual environment
    • Verify the installation
  • Quickstart
    • Input file format
    • Command line
    • Python API
      • Linear Manhattan plot (single trait)
      • Multi-track linear Manhattan plot
      • Circular (Circos-style) Manhattan plot
      • QQ plots
    • Mixed genome builds with liftover
    • Next steps

User Guide

  • Command-Line Interface
    • Input / output options
    • Column auto-detection options
    • Plotting behaviour options
    • QQ plot options
    • Example commands
      • Single-trait linear Manhattan plot
      • Three-trait stacked linear Manhattan plot
      • Circular Manhattan plot
      • Manhattan plot with companion QQ plots
      • Supplying per-file genome builds
  • Python API Tutorial
    • Python API for the pycmplot package
      • Installation
      • Import the package functions
      • Getting help
    • Example plotting
      • Important notes
      • Generating a linear plot
        • No highlighting of significant loci
      • Generating a linear plot
      • Highlighting significant loci and annotating by SNP
        • Highlighting by a different p-value threshold and changing plot colors and removing track labels
      • Generating circular plots
        • Controling the inner circle size
      • Ensuring all highlighted loci are also annotated
        • Explicitly speficying directory where output files should be stored
      • # Handling other use cases and QQ-plots
      • Summary stats without BUILD column and no build information provided
      • ## Supplying builds with summary stats
      • ## QQ-Plotting
        • Overlaying multiple
        • Separate qq-plots saved in separate figures
        • Combined multi-panel
        • Flexible handling of each qq-plot using the base plot_qq_single function directly
        • Or overlay them by simply using the same axis
        • This gives us the flexibility to place multiple overlay plots on one figure
      • # Final Notes

API Reference

  • API Reference
    • pycmplot.io
      • pycmplot.io
      • auto_thin_for_manhattan()
      • detect_delimiter()
      • generate_random_string()
      • get_file_header()
      • get_output_paths()
      • get_sumstats_and_merged_sector_list()
      • prep_pycmplot_input_info()
      • resolve_delimiter()
      • smart_open()
      • strip_comma_separated_input_streams()
    • pycmplot.stats
      • pycmplot.stats
      • get_highlight_snps()
      • get_lead_snps()
    • pycmplot.annotation
      • pycmplot.annotation
        • Gene reference files
      • get_annotation_column()
      • get_hits_summary_table()
    • pycmplot.liftover
      • pycmplot.liftover
        • Supported conversions
        • Resource configuration
      • liftover_hg18_to_hg38()
      • liftover_hg19_to_hg38()
      • liftover_position()
    • pycmplot.plotting
      • pycmplot.plotting.linear
        • pycmplot.plotting.linear
        • plot_linear()
        • plot_linearm()
      • pycmplot.plotting.circular
        • pycmplot.plotting.circular
        • compute_track_radii_dict()
        • plot_circosm()
        • plot_circular()
      • pycmplot.plotting.qq
        • plot_qq_combined()
        • plot_qq_overlay()
        • plot_qq_separate()
        • plot_qq_single()
        • thin_pvals()
    • pycmplot.constants
      • pycmplot.constants
        • Contents
    • pycmplot.resources
      • pycmplot.resources
        • Resolution order
      • ResourceConfig
        • ResourceConfig.chain_hg18_hg38
        • ResourceConfig.chain_hg19_hg38
        • ResourceConfig.geneinfo_hg19
        • ResourceConfig.geneinfo_hg38
        • ResourceConfig.require()

Project Info

  • Changelog
    • [0.2.8] — 2026-05-30
    • 0.2.7 — 2026-04-27
    • 0.2.5 — 2026-04-20
    • 0.2.2 — 2026-04-18
    • 0.2.1 — 2026-04-16
    • 0.1.9 — 2026-04-14
    • 0.1.8 — 2026-04-14
    • 0.1.0 — 2026-04-18
  • Contributing
    • Reporting issues
    • Development setup
    • Building the documentation locally
    • Code style
    • Docstrings
  • License
pycmplot
  • Python Module Index

Python Module Index

p
 
p
- pycmplot
    pycmplot.annotation
    pycmplot.constants
    pycmplot.io
    pycmplot.liftover
    pycmplot.plotting.circular
    pycmplot.plotting.linear
    pycmplot.plotting.qq
    pycmplot.resources
    pycmplot.stats

© Copyright 2026, Kevin Esoh.

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