Plugy: Python module for plug microfluidics data analysis

Issues

Feedback, questions, bug reports are welcome: https://github.com/saezlab/plugy/issues

Installation

Imports & Setup

You can now install plugy as a package using pip in your conda environment. To install pip in your conda environment run the following lines on your bash or conda prompt.

# Activate your conda environment replacing 'YOUR_ENVIRONMENT' with the name of your environment
conda activate YOUR_ENVIRONMENT

# Install pip git support, such that plugy can be directly installed from gitlab
conda install pip git

# Install plugy into your environment
pip install git+https://github.com/saezlab/plugy@master

# If you want to use the latest development version use this instead
pip install --force-reinstall git+https://github.com/saezlab/plugy@dev

Quick start

This notebook will show you how to run a plugy based analysis of a drug combination Braille display microfluidics experiment.

First, make sure your Python shell is running in the working directory where (or in its subdirectories) you have the data and where you want to save the results.

The simplest workflow, which is sufficient most of the times, looks like this:

import plugy
exp = plugy.PlugExperiment()
exp.main()

Further settings, parameters can be passed to PlugExperiment:

import plugy
exp = plugy.PlugExperiment(
    peak_min_threshold = 0.02,
    barcoding_param = {
        'times': (.2, 4.0),
    },
    heatmap_second_scale = 'pos-ctrl',
)
exp.main()

If you want to interact with the data use the contents of the exp object. It contains all the plug, pmt, channel and sequence data that was used in the analysis. For example, a pandas.DataFrame containing the statistics for each sample:

exp.sample_statistics

Tutorial

You can find more examples in the plugy guide: https://github.com/saezlab/plugy/blob/master/notebooks/plugy_guide.ipynb

Development history

https://github.com/saezlab/plugy/blob/master/NEWS.md