.. _api_plotting:

pycmplot.plotting
=================

The plotting subpackage contains three modules: one for linear (stacked)
Manhattan plots, one for circular (Circos-style) Manhattan plots, and one
for QQ plots.

pycmplot.plotting.linear
-------------------------

Generates single- and multi-track stacked linear Manhattan plots with
optional significance lines, locus highlighting, cluster-aware label
spreading, and intelligent arrow-angle calculation for gene annotations.

.. currentmodule:: pycmplot.plotting.linear

.. automodule:: pycmplot.plotting.linear
   :members:
   :undoc-members:
   :show-inheritance:

pycmplot.plotting.circular
---------------------------

Generates multi-track Circos-style circular Manhattan plots. Track radii
are computed automatically to give each track proportional visual weight
relative to its data range.

.. currentmodule:: pycmplot.plotting.circular

.. automodule:: pycmplot.plotting.circular
   :members:
   :undoc-members:
   :show-inheritance:

pycmplot.plotting.qq
---------------------

Produces QQ plots with 95 % beta-distribution confidence bands, optional
genome-wide significance lines, and genomic inflation (λ) annotation.
Supports log-uniform point thinning for fast plotting of large datasets.
Three high-level layouts are provided: combined (grid of per-trait
panels), separate (one file per trait), and overlay (all traits on one
shared axes).

.. currentmodule:: pycmplot.plotting.qq

.. automodule:: pycmplot.plotting.qq
   :members:
   :undoc-members:
   :show-inheritance: