Repertoire analysis

Published

May 28, 2024

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 run1 samples.
Figure 3: UpSet plot for run2 samples.
Figure 4: UpSet plot for run3 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 5: Renyi entropy curves

VJ gene usage

Figure 6: 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 7: Chord diagram for run1_bio1_tech1 sample
Figure 8: Chord diagram for run1_bio1_tech2 sample
Figure 9: Chord diagram for run1_bio2_tech1 sample
Figure 10: Chord diagram for run1_bio2_tech2 sample
Figure 11: Chord diagram for run2_bio1_tech1 sample
Figure 12: Chord diagram for run2_bio1_tech2 sample
Figure 13: Chord diagram for run2_bio2_tech1 sample
Figure 14: Chord diagram for run2_bio2_tech2 sample
Figure 15: Chord diagram for run3_bio1_tech1 sample
Figure 16: Chord diagram for run3_bio1_tech2 sample
Figure 17: Chord diagram for run3_bio2_tech1 sample
Figure 18: Chord diagram for run3_bio2_tech2 sample

CDR3 sequence length analysis

Figure 19: Histograms of CDR3 AA sequences’ length

Appendix

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