Marker Overlap Calculator

This function is designed for quality control (QC) in high-plex translational single-cell datasets, such as those obtained from CODEX (Co-Detection by indEXing), IMC (Imaging Mass Cytometry) or other single cell based technologies. It specifically evaluates the overlap of markers that are typically considered 'mutually exclusive' within individual cells. This assessment helps in identifying potential issues with marker specificity, staining quality, or data processing algorithms, ensuring the reliability and accuracy of the dataset analysis.

Overview

This Python script calculates the overlap percentages between various markers in cell data. It requires a DataFrame (df) and a list of markers of interest. The script outputs the counts and percentages of overlaps, facilitating insights into marker co-expression that might indicate staining errors or other anomalies in sample preparation or data capture.

Requirements

• Python: Ensure Python is installed on your system.
• Pandas library: Required for handling data. Make sure to install this Python library.

Installation

Before running the script, you need to install the necessary Python packages:

pip install pandas

Sample df

df = pd.DataFrame({
    'CD45': ['Other', 'CD45', 'CD45'],
    'CD31': ['CD31', 'Other', 'CD31'],
    'CK': ['Other', 'CK', 'Other'],
    'CD3': ['CD3', 'Other', 'CD3']
})

## List of markers of interest
markers = ['CD45', 'CD31', 'CK', 'CD3']

## Usage
Run the script with Python. 

python overlap_calculator.py