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TCRi

Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing

alt text

https://www.biorxiv.org/content/10.1101/2022.10.01.510457v1

Install:

python3 -m venv tvenv
source tvenv/bin/activate
python3 setup.py install

Example code found in /examples.

Basics

Compute joint distribution with TCRi on anndata processed with GeneVector.

import tcri

sample_column="sample"
condition_column="source"
phenotype_column="genevector"

tcri.pp.joint_distribution(adata,
                           sample_column=sample_column, 
                           condition_column=condition_column, 
                           phenotype_column=phenotype_column)

Each metric has an associated plotting function

  1. Clonotypic Entropy 
    tcri.metrics.clonotypic_entropy(adata)
tcri.pl.clonotypic_entropy(adata)
  2. Phenotypic Entropy 
    tcri.metrics.phenotypic_entropy(adata)
tcri.pl.phenotypic_entropy(adata)
  3. Phenotypic Flux 
    tcri.metrics.phenotypic_flux(adata,from_this="TP1",to_that="TP2")
tcri.pl.phenotypic_flux(adata,from_this="TP1",to_that="TP2")