pymatviz 0.4.1

A toolkit for visualizations in materials informatics

pymatviz

A toolkit for visualizations in materials informatics.

Note: This project is not associated with or endorsed by pymatgen, but aims to complement it by adding additional plotting functionality.

Installation

pip install pymatviz

Elements

See pymatviz/elements.py.

ptable_heatmap(compositions, log=True)	ptable_heatmap_ratio(comps_a, comps_b)

Sunburst

See pymatviz/sunburst.py.

spacegroup_sunburst([65, 134, 225, ...])	spacegroup_sunburst([65, 134, 225, ...], show_values="percent")

Structure

See pymatviz/struct_vis.py.

plot_structure_2d(pmg_struct)	plot_structure_2d(pmg_struct, show_unit_cell=False, site_labels=False)

Histograms

See pymatviz/histograms.py.

spacegroup_hist([65, 134, 225, ...])	spacegroup_hist(["C2/m", "C2/m", "Fm-3m", ...])
residual_hist(y_true, y_pred)	hist_elemental_prevalence(compositions, log=True, bar_values='count')

Parity Plots

See pymatviz/parity.py.

density_scatter(xs, ys, ...)	density_scatter_with_hist(xs, ys, ...)
density_hexbin(xs, ys, ...)	density_hexbin_with_hist(xs, ys, ...)
scatter_with_err_bar(xs, ys, yerr, ...)	residual_vs_actual(y_true, y_pred, ...)

Uncertainty Calibration

See pymatviz/quantile.py.

qq_gaussian(y_true, y_pred, y_std)	qq_gaussian(y_true, y_pred, y_std: dict)

Ranking

See pymatviz/ranking.py.

err_decay(y_true, y_pred, y_std)	err_decay(y_true, y_pred, y_std: dict)

Cumulative Error and Residual

See pymatviz/cumulative.py.

cum_err(preds, targets)	cum_res(preds, targets)

Classification Metrics

See pymatviz/relevance.py.

roc_curve(targets, proba_pos)	precision_recall_curve(targets, proba_pos)

Correlation

See pymatviz/correlation.py.

marchenko_pastur(corr_mat, gamma=ncols/nrows)	marchenko_pastur(corr_mat_significant_eval, gamma=ncols/nrows)

Migrating from ml-matrics to pymatviz

This library was renamed from ml-matrics to pymatviz between versions 0.3.0 and 0.4.0. To update existing Python files that import ml-matrics in place, run the following commands. On Linux:

find . -iname '*.py' -o -iname '*.ipynb' | xargs sed -i 's/from ml_matrics import/from pymatviz import/g'
find . -iname '*.py' -o -iname '*.ipynb' | xargs sed -i 's/from ml_matrics./from pymatviz./g'
find . -iname '*.py' -o -iname '*.ipynb' | xargs sed -i 's/import ml_matrics/import pymatviz/g'

On Mac, replace sed -i with sed -i "".

Glossary

1. Residual y_res = y_true - y_pred: The difference between ground truth target and model prediction.
2. Error y_err = abs(y_true - y_pred): Absolute error between target and model prediction.
3. Uncertainty y_std: The model's estimate for its error, i.e. how much the model thinks its prediction can be trusted. (std for standard deviation.)