TCRi

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

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 GeneVectgor.

import tcri

sample_column="sample"
condition_column="source"
clonotype_column = "IR_VDJ_1_junction_aa"
phenotype_column="genevector"

tcri.pp.joint_distribution(adata,
                           sample_column=sample_column, 
                           condition_column=condition_column,
                           clonotype_column=clonotype_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")