General genetics/genomics utilities.
Project description
genetools: single-cell analysis recipes (work in progress)
Plot gallery
Other features
- Compare clustering results by computing co-clustering percentage.
- Map marker genes against reference lists to find names for your clusters.
- pandas shotrcuts:
- Split single cell barcodes conveniently.
- Defensive pandas merging and concatenation methods with strict correctness checks.
Full documentation: https://genetools.maximz.com.
Install
Run pip install --upgrade 'genetools[scanpy]'
.
Or if you don't use scanpy: pip install --upgrade genetools
.
Usage
To use genetools in a project, add import genetools
. Review the documentation and the tests for examples.
Development
Setup:
git clone git://github.com/maximz/genetools
cd genetools
pip install --upgrade pip wheel
pip install -r requirements_dev.txt
pre-commit install
Common commands:
# lint
make lint
# one-time: generate test anndata, and commit so we have reproducible tests in CI
rm -r data
make regen-test-data
# run tests locally
# this is done in a debian-based docker image to ensure image style matches what Github Actions CI will produce
# failing image snapshot tests are recorded in tests/results/
make build-docker-test-image # whenever requirements_dev.txt change
make test
# generate baseline figures (also happens in docker)
make regen-snapshot-figures
# regenerate test data, and baseline figures (also happens in docker)
make regen-test-data
# run tests locally without docker, therefore omitting the snapshot tests
# (the @snapshot_image tests are still executed but the images are not compared. the @pytest.mark.snapshot_custom are skipped altogether.)
make test-without-figures
# docs
make docs
# bump version before submitting a PR against master (all master commits are deployed)
bump2version patch # possible: major / minor / patch
# also ensure CHANGELOG.md updated
CI:
- Main: Github Actions
- Docs: https://app.netlify.com/sites/genetools
Changelog
0.7.0
0.6.0
- Two new functions to customize tick labels on any existing plot:
wrap_tick_labels
: add text wrappingadd_sample_size_to_labels
: add group sample sizes with a(n=N)
suffix
- Make writing PDF figures a deterministic process and make the PDF text editable.
- Scatterplot improvements:
- Adjust default marker shape and size to work better for most plots.
- Adjust HueValueStyle so that an explicit marker size is not specified there, only a marker size scaling factor. The scatterplot itself is responsible for defining the base marker size, while the palette of HueValueStyles should be drawable at any marker size.
- Change legends so that only one marker is drawn to indicate a group's style.
0.5.0 (2022-01-10)
- Improve scatter plots and stacked bar plots.
- Introduce
HueValueStyle
for granular styling of each hue.
0.4.0 (2020-07-22)
- Centered log ratio (CLR) normalization for Cite-seq protein data.
0.3.0 (2020-06-03)
- Pandas helpers for easier normalization
0.2.0 (2020-06-03)
- Far faster implementation of
stats.coclustering
- Introducing
helpers.make_slurm_command
- Global submodule import (no longer need to import submodules individually)
0.1.0 (2020-03-06)
- First release on PyPI.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
genetools-0.7.3.tar.gz
(1.8 MB
view hashes)
Built Distribution
Close
Hashes for genetools-0.7.3-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b3a397259d7c32de6a314eed485efc8f3d9fc25a8dab3dd070ae723942f7fdc8 |
|
MD5 | d871292320982c5cc55f49ffa8344292 |
|
BLAKE2b-256 | 0ca3da63daa467f864cfd3815aa48cd13903bcaa7ddde61edca26def4291fe39 |