Adding TCRDist3 Functionality to Cirro

[RachelKarchin]

This the path to the TCRdist docker: https://tcrdist3.readthedocs.io/en/latest/docker.html (quay.io/kmayerb/tcrdist3:0.1.9) we are planning to base on.

[yuvalel]

Basic functionality requested - a user has a few TCR samples and want to explore the internal distances in each samples. This could be a biomarker of either response or potential to response and could be correlated vs clinical covariates.
Specifically we would like the user to be able to visualize distances within a repertoire sample(s) according to this breakdown:

1. Input - repertoire sample (minimal example - just bulk beta CDR3s), output- distance matrix. Calculate every pairwise distance in the sample and output it as a matrix.
2. Visualize distance matrix as a heatplot with or without clustering
3. Histogram the distances and plot as a distribution over distance.

[KevinMLanderos]

Title: "Adding TCRdist3 Functionality to Cirro"

Introduction: Implementing TCRdist3 to TCRtoolkit will aid analysis when having TCR samples and want to explore the internal distances in each samples. Results could show a biomarker of either response or potential to response and could be correlated vs clinical covariates.

Outline of problem to be addressed: Specifically, we would like the user to calculate every pairwise distance in a bulk sample and output it as a matrix. We would also like to be able to visualize distances as a heatplot with or without clustering.

Expected inputs:

• bulk-TCR repertoire data in tabular format (minimal example: CDR3b); can include V,J genes info and metadata.
• Parameters: organism, chains (beta), etc...

Commands to be run/implemented:
(TCRdist3 documentation: https://tcrdist3.readthedocs.io/en/latest/tcrdistances.html)

• TCRrep: Will give tcr distances
• Plotting function for heatmap (e.g. pheatmap in R)
• Dendogram function for clustering

Expected outputs:

• Distance matrix
• Clustering result: Computed from distances
• Heatmap of the TCR distance matrix