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https://github.com/ssi-dk/cd-mrg-plateplanner
Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.
https://github.com/ssi-dk/cd-mrg-plateplanner
Last synced: 3 days ago
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Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.
- Host: GitHub
- URL: https://github.com/ssi-dk/cd-mrg-plateplanner
- Owner: ssi-dk
- License: mit
- Created: 2023-02-17T16:54:48.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-07-30T10:35:23.000Z (4 months ago)
- Last Synced: 2024-11-05T23:51:40.346Z (9 days ago)
- Language: Python
- Size: 45.3 MB
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
[](https://pypi.org/project/plate-planner)
[](https://pypi.org/project/plate-planner)
[](https://github.com/ssi-dk/CD-MRG-PlatePlanner/actions/workflows/pages/pages-build-deployment)
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-----
- **Dynamic QC Sample Patterns**: Create plate layouts with customizable QC sample patterns.
- **Flexible Sample Distribution**: Distribute samples within groups across plates, accommodating variable numbers of samples per group.
- **Non-Split/Split Group Handling**: Control over distributing samples within groups without splitting them over plates or splitting when necessary.
- **Customizable Run Lists & Plate Visualizations**: Generate run lists and visualize plate assignments.
- **Block Randomization**: Perform sample randomizaition or sample block randomization to prevent run order bias.
## Installation
To install PlatePlanner, simply run:
```console
pip install plate-planner
```
## Documentation
For more detailed documentation, visit [PlatePlanner Documentation](https://ssi-dk.github.io/CD-MRG-PlatePlanner/).
## Quick Start Guide
Here's a quick example of how to use PlatePlanner:
```py
from plate-planner import Study, QCPlate
# Create a study and load your file with sample records (csv, xls/xlsx)
study_with_qc = Study(name="cancer")
study_with_qc.load_specimen_records(
records_file="./data/study_samples.csv",
sample_group_id_column="pair_ID",
sample_id_column="specimen_ID"
)
# Block randomize groups
study_with_qc.randomize_order(case_control=True, reproducible=False)
# Distribute samples to a 96-well plate with QC samples as defined in the toml file
qc_plate = QCPlate(plate_dim=(8, 12), QC_config="./data/plate_config_dynamic.toml")
study_with_qc.distribute_samples_to_plates(plate_layout=qc_plate)
# Create visualization for plate 3
fig = study_with_qc[2].as_figure(
color_metadata_key="organ",
annotation_metadata_key="date_of_birth",
rotation=45,
)
```
```py
#mshow distribution of sample attribute across all plates
fig = study_with_qc.plot_attribute_plate_distributions(attribute="organ", normalize=True, plt_style="fivethirtyeight")
```
## Contributing
We welcome contributions to PlatePlanner! Please read our Contributing Guidelines for more information on how to get involved.
## License
PlatePlanner is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.