plate-planner 0.1.5

A tool to create and visualize sample layouts for multiwell plates.

• 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: Utilize block randomization to prevent run order bias.
• Stratified Randomization (Upcoming): This feature, once implemented, will ensure balanced distribution of group attributes across LC-MS plates or batches.

Installation

To install PlatePlanner, simply run:

pip install plate-planner

Documentation

For more detailed documentation, visit PlatePlanner Documentation.

Quick Start Guide

Here's a quick example of how to use PlatePlanner:

from plate_layout import Study, QCPlate

# Create a study and load your file with sample records (csv, xls/xlsx)
study = Study(name="cancer")
study.load_specimen_records(
    records_file="./data/study_samples.csv",
    sample_group_id_column="pair_ID",
    sample_id_column="specimen_ID"
)

# Block randomize groups
study.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.distribute_samples_to_plates(plate_layout=qc_plate)

# Create visualization for plate 3
fig = study[3].as_figure(
    color_metadata_key="organ",
    annotation_metadata_key="object",
    rotation=45,
    fontsize=8
)

fig = study[3].to_layout_figures(
    annotation_metadata_key="sample_name",
    color_metadata_key="sample_code",
    file_format="png"
)

Visualization Examples

Here are some examples of plate visualizations created using PlatePlanner:

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 license.