FlowKit 0.1.0

Flow Cytometry Toolkit

Overview

FlowKit is an intuitive Python toolkit for flow cytometry analysis and visualization, including GatingML 2.0 support. Features include:

• Reading Flow Cytometry Standard data (FCS files), including FCS versions:
  • 2.0
  • 3.0
  • 3.1
• Exporting FCS data in any of the following formats:
  • A new FCS 3.1 file, with modified metadata and/or filtered events
  • NumPy array
  • Pandas DataFrame
  • CSV text file
• Compensating FCS events using spillover matrices in multiple formats:
  • As the $SPILL or $SPILLOVER keyword value format
  • FlowJo tab-delimited text format
  • NumPy array
  • GatingML 2.0 spectrumMatrix XML element
• Tranformation of original or compensated events in a variety of transforms used in the flow community:
  • Logicle
  • Inverse hyperbolic sine (arcsinh)
  • Hyperlog
  • Logarithmic
  • Channel ratios
  • Linear
• Optional, automatic filtering of negative scatter events and/or anomalous events
• Visualizing FCS event data:
  • Histogram of single channel data with a Gaussian kernel density estimate curve
  • Contour density plot of two channels
  • Interactive scatter plot of two channels
  • Interactive scatter plot matrix of any combination of channels

Requirements

FlowKit supports Python version 3.6 or above. All dependencies are installable via pip, and include:

• flowio >= 0.9.3
• flowutils >= 0.6.8
• numpy >= 0.15
• scipy >= 1.0
• pandas >= 0.19
• matplotlib >= 3.0
• seaborn >= 0.9
• bokeh >= 1.0
• lxml >= 4.2
• anytree >= 2.4

Installation

From PyPI

pip install flowkit

From source

git clone https://github.com/whitews/flowkit
cd flowkit
python setup.py install

Usage

Check out the example notebooks:

• General Overview
• Applying Transforms to a Sample