Fig. 3 | Nature Communications

Fig. 3

From: Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets

Fig. 3

Effects of perplexity and EE factor adjustments on t-SNE visualization of cytometry data. a, b KLD, KLDRC, and t-SNE biaxial plots generated with varying EE factor values. c, d KLD, KLDRC, and t-SNE biaxial plots generated with varying perplexity. Graphs showing KLD and KLDRC change over iteration time are color-labeled to distinguish curves corresponding to experiment perturbations. Color overlays on t-SNE plots correspond to cell type classes labeled as in Figs. 1, 2. Representative examples of multiple runs with varying seed values are shown

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