cbrviz
Small, composable Matplotlib building blocks for statistical figures — strip/box plots with p-value annotation, KDE ridges and split violins, XY panels with correlation and zoom, dot plots / correlation plots, and Kaplan-Meier curves.
Every class is a thin wrapper around a validated DataFrame plus a handful of
ax-based draw methods, so you keep full control of the figure.
Install
pip install cbrviz
Two statistics back-ends are optional:
pip install "cbrviz[survival]" # KME (scikit-survival)
pip install "cbrviz[stats]" # StripBox.calc_pairwise_p (scikit-posthocs)
pip install "cbrviz[all]" # both
Quickstart
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from cbrviz import StripBox
rng = np.random.default_rng(0)
df = pd.DataFrame({
"expression": np.concatenate([rng.normal(m, 1, 30) for m in (5.0, 6.5, 5.2)]),
"genotype": np.repeat(["WT", "KO", "Rescue"], 30),
})
sb = StripBox(df, s1_order=["WT", "KO", "Rescue"])
fig, ax = plt.subplots()
sb.boxplt(ax=ax, showfliers=False)
sb.add_strips(ax=ax, s=12)
sb.add_global_p(ax=ax)
sb.calc_pairwise_p(posthoc_method="dunn") # needs cbrviz[stats]
sb.add_pair_p("WT", "KO", ax=ax)
usage() — a runnable example for every class
Not sure how a class works? Ask it:
>>> from cbrviz import Ridge
>>> Ridge.usage()
# Typical use of Ridge
import numpy as np
...
Modules
| import | what it draws |
|---|---|
StripBox, SplitStripBox, PairedStripBox |
box + strip plots, global & pairwise p-values |
KDE, KDE2D, Ridge, SplitViolin |
1-D / 2-D kernel density, ridgeline, split violin |
XYview, XYpairs, XYzoom |
scatter with correlation / regression / labelled points / zoom inset |
Dotplot, Corrplot |
grid dot plots and clustered correlation plots |
KME |
Kaplan-Meier curves, log-rank, pairwise log-rank heatmap (needs cbrviz[survival]) |
resolve_categories, resolve_colors |
helpers for level ordering and palette resolution |
Heatmap (cbrviz.heatmap) is a placeholder and raises NotImplementedError.
Development
git clone https://github.com/fossbert/cbrviz
cd cbrviz
pip install -e ".[test]"
pytest
License
MIT — see LICENSE.
1 maintainer
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