domains / families / science / repertoire-visualization

repertoire-visualization

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Draws TCR/BCR repertoire figures - V-J chord/circos, CDR3 spectratype, clonal-space stratification, clonal tracking across timepoints, rarefaction/extrapolation curves, overlap heatmaps, and clonotype-similarity networks - and encodes how to read them. Use when choosing between a raw Shannon bar and a rarefaction curve for a diversity comparison; deciding a depth-robust overlap metric (Morisita-Horn) vs a set metric (Jaccard) for a heatmap; setting the distance threshold that defines a clonotype-similarity network; interpreting a Gaussian vs skewed spectratype as polyclonal vs clonally expanded; or laying out clonal-space and clone-tracking plots. Covers VDJtools PlotFancyVJUsage/RarefactionPlot, R circlize and iNEXT, and matplotlib/seaborn recipes.

When to use

• V-J chord/circos
• CDR3 spectratype
• clonal-space stratification
• clonal tracking across timepoints
• rarefaction/extrapolation curves
• overlap heatmaps
• clonotype-similarity networks
• choosing between raw Shannon bar and rarefaction curve

When not to use

• comparing raw usage across primer sets/platforms

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