# genetools: single-cell analysis recipes (work in progress)
[](https://pypi.python.org/pypi/genetools)
[](https://github.com/maximz/genetools/actions/workflows/ci.yaml)
[](https://genetools.maximz.com)
[](https://github.com/maximz/genetools)
[](https://codecov.io/gh/maximz/genetools)
## Plot gallery
<table>
<tr>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_scatterplot_discrete)
</td>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_stacked_bar_plot)
</td>
</tr>
<tr>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_scatterplot_continuous)
</td>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_stacked_bar_plot_autocompute_frequencies)
</td>
</tr>
<tr>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%20test_dotplot)
</td>
<td>
[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_relative_density)
</td>
</tr>
</table>
## 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](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](https://genetools.maximz.com) and the [tests](https://github.com/maximz/genetools/tree/master/tests) for examples.
## Development
Setup:
```bash
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:
```bash
# 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](https://app.netlify.com/sites/genetools)
# Changelog
## 0.7.0
* Many new stats, plotting, and helper functions. See PRs [#24](https://github.com/maximz/genetools/pull/24) and [#73](https://github.com/maximz/genetools/pull/73).
## 0.6.0
* Two new functions to customize tick labels on any existing plot:
* `wrap_tick_labels`: add text wrapping
* `add_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.
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"description": "# genetools: single-cell analysis recipes (work in progress)\n\n[](https://pypi.python.org/pypi/genetools)\n[](https://github.com/maximz/genetools/actions/workflows/ci.yaml)\n[](https://genetools.maximz.com)\n[](https://github.com/maximz/genetools)\n[](https://codecov.io/gh/maximz/genetools)\n\n## Plot gallery\n\n<table>\n<tr>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_scatterplot_discrete)\n\n</td>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_stacked_bar_plot)\n\n</td>\n</tr>\n\n<tr>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_scatterplot_continuous)\n\n</td>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_stacked_bar_plot_autocompute_frequencies)\n\n</td>\n</tr>\n\n<tr>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%20test_dotplot)\n\n</td>\n<td>\n\n[](https://github.com/maximz/genetools/blob/master/tests/test_plots.py#:~:text=def%test_relative_density)\n\n</td>\n</tr>\n\n</table>\n\n## Other features\n\n* Compare clustering results by computing co-clustering percentage.\n* Map marker genes against reference lists to find names for your clusters.\n* pandas shotrcuts:\n * Split single cell barcodes conveniently.\n * Defensive pandas merging and concatenation methods with strict correctness checks.\n\nFull documentation: [https://genetools.maximz.com](https://genetools.maximz.com).\n\n## Install\n\nRun `pip install --upgrade 'genetools[scanpy]'`.\n\nOr if you don't use scanpy: `pip install --upgrade genetools`.\n\n## Usage\n\nTo use genetools in a project, add `import genetools`. Review the [documentation](https://genetools.maximz.com) and the [tests](https://github.com/maximz/genetools/tree/master/tests) for examples.\n\n## Development\n\nSetup:\n\n```bash\ngit clone git://github.com/maximz/genetools\ncd genetools\npip install --upgrade pip wheel\npip install -r requirements_dev.txt\npre-commit install\n```\n\nCommon commands:\n\n```bash\n# lint\nmake lint\n\n# one-time: generate test anndata, and commit so we have reproducible tests in CI\nrm -r data\nmake regen-test-data\n\n# run tests locally\n# this is done in a debian-based docker image to ensure image style matches what Github Actions CI will produce\n# failing image snapshot tests are recorded in tests/results/\nmake build-docker-test-image # whenever requirements_dev.txt change\nmake test\n\n# generate baseline figures (also happens in docker)\nmake regen-snapshot-figures\n\n# regenerate test data, and baseline figures (also happens in docker)\nmake regen-test-data\n\n# run tests locally without docker, therefore omitting the snapshot tests\n# (the @snapshot_image tests are still executed but the images are not compared. the @pytest.mark.snapshot_custom are skipped altogether.)\nmake test-without-figures\n\n# docs\nmake docs\n\n# bump version before submitting a PR against master (all master commits are deployed)\nbump2version patch # possible: major / minor / patch\n\n# also ensure CHANGELOG.md updated\n```\n\nCI:\n\n- Main: Github Actions\n- Docs: [https://app.netlify.com/sites/genetools](https://app.netlify.com/sites/genetools)\n\n\n# Changelog\n\n## 0.7.0\n\n* Many new stats, plotting, and helper functions. See PRs [#24](https://github.com/maximz/genetools/pull/24) and [#73](https://github.com/maximz/genetools/pull/73).\n\n## 0.6.0\n\n* Two new functions to customize tick labels on any existing plot:\n * `wrap_tick_labels`: add text wrapping\n * `add_sample_size_to_labels`: add group sample sizes with a `(n=N)` suffix\n* Make writing PDF figures a deterministic process and make the PDF text editable.\n* Scatterplot improvements:\n - Adjust default marker shape and size to work better for most plots.\n - 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.\n - Change legends so that only one marker is drawn to indicate a group's style.\n\n## 0.5.0 (2022-01-10)\n\n* Improve scatter plots and stacked bar plots.\n* Introduce `HueValueStyle` for granular styling of each hue.\n\n## 0.4.0 (2020-07-22)\n\n* Centered log ratio (CLR) normalization for Cite-seq protein data.\n\n## 0.3.0 (2020-06-03)\n\n* Pandas helpers for easier normalization\n\n## 0.2.0 (2020-06-03)\n\n* Far faster implementation of `stats.coclustering`\n* Introducing `helpers.make_slurm_command`\n* Global submodule import (no longer need to import submodules individually)\n\n## 0.1.0 (2020-03-06)\n\n* First release on PyPI.\n",
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