Explanation of S, H, and E

S Richness (Unique Clonotypes) - The number of distinct clonotypes (unique DNA sequences) detected in a sample. It reflects how many different clonotypes are present, regardless of their abundance.

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H Shannon Diversity Index - A measure of both richness and evenness. It is calculated as:
H = −Σ (pᵢ × ln pᵢ) where pᵢ is the proportional abundance of clonotype i (countᵢ / total). Higher H indicates greater diversity—many clonotypes with balanced frequencies rather than domination by a few.

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E Shannon’s Equitability (Evenness) - A normalized measure of how evenly the clonotypes are distributed. It is computed as:
E = H / ln(S)
Values range from 0 to 1:
– 1 = perfectly even distribution (all clonotypes have equal abundance)
– 0 = highly uneven distribution (dominated by few clonotypes).

Interpreting Shannon’s Diversity

• Shannon Diversity (H) captures both the number of clonotypes and their relative abundance.

  • In immune repertoire analysis, a high H means the repertoire is diverse — the immune system is responding to many distinct antigens or maintaining broad coverage.

  • A low H indicates clonal expansion — a few clonotypes dominate, typical in antigen-driven responses or restricted repertoires.

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• Shannon’s Equitability (E) isolates the evenness component of diversity.

  • If E ≈ 1: all clonotypes are represented similarly → balanced or polyclonal repertoire.

  • If E ≈ 0: few clonotypes dominate → skewed or clonal repertoire.