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Fig. 3 | Genome Medicine

Fig. 3

From: A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status

Fig. 3

Diversity profiles recover the underlying frequency distribution to a large extent. a Simulation of 1000 clonal frequency (Zipf) distributions of varying degree of clonal expansion (Zipf-alpha = 0.1, Zipf-B [0.001, 0.1]), but equal clonal composition. Distributions were colored by extent of clonal expansion (blue, low clonal expansion; red, high clonal expansion). b Diversity profiles of Zipf-distributions (a) were plotted for alpha values ranging from 0 to 10. Diversity profiles were colored by the respective Zipf-distribution. c Zipf-distributions (a) were hierarchically clustered based on Pearson correlation distance in order to only take into account the shape of the distributions. Hierarchical clustering was visualized using heatmaps, in which each tile represents the Pearson correlation coefficient between any two distributions. Row and column color (blue, red) bars indicate the respective degree of clonal expansion of each distribution as shown in (a). d Diversity profiles of Zipf-distributions (a) were hierarchically clustered based on Pearson correlation distance in order to only take into account relative clonal expansion differences. e The cophenetic correlation of the dendrograms of Zipf-distributions (c) and of Diversity profiles (d) was determined as a function of a growing [accumulating] number of alpha-values used — the number of alpha values was varied between 2 and 51 within an alpha range of 0 to 10 (step size of 0.2). The cophenetic correlation (r) between dendrograms of frequency distributions and Diversity profiles increases with increasing number of alpha values used reaching r ≈ 0.94 for 40 and r ≈ 0.82 for 51 alpha values used. f Color bars as used in heatmaps in (c) and (d) are shown to visualize the correspondence of clustering of Zipf distributions and Diversity profiles for the two extreme cases of the number of alpha values used: 2 (blue arrow) and 51 (red arrow)

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