Repertoire analysis

Published

November 12, 2025

Count distribution

Figure 1: # of clone distribution per sample

Shared clonotypes per group

The figures below have clonotypes repeated \(\geq\) 5 times

Figure 2: UpSet plot for group1 samples.

Diversity analysis

The diversity is generalized to the Renyi entropy defined as:

\[ H(\alpha) = \frac{1}{1 - \alpha} \log \left( \sum_{i=1}^n p_i^\alpha \right) \]

where:

  • \(n\) is the total number of unique clonotypes
  • \(p_i\) is the clonotype frequency for clonotype \(i\)
Figure 3: Renyi entropy curves

VJ gene usage

Figure 4: Gene frequency usage per group

VJ genes paired usage

The figures use the clonotypes annotated by unique V and J genes, and ignoring the genes that portray less than 15% of the total number of annotated clonotypes

Figure 5: Chord diagram for sample1 sample
Figure 6: Chord diagram for sample2 sample

CDR3 sequence length analysis

Figure 7: Histograms of CDR3 AA sequences’ length

Appendix

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 date     2025-11-12
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