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Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference

Fig 3

F-informed MDS is robust to the choice of hyperparameters.

(A) Shepard plots comparing pairwise distances from F-informed MDS (F-MDS) and supervised MDS (superMDS) under both zero (metric MDS) and nonzero hyperparameter settings (, ). Distances in the original high-dimensional space were computed using Bray-Curtis dissimilarity; distances in the two-dimensional embedding used Euclidean metric. (B) For each method, the Pearson correlation coefficient was calculated between original and embedded distances. (C) Normalized stress (Stress-1) was computed for each embedding. Analysis used semisynthetic datasets with N = 200 (see the “Semisynthetic data” section of the Methods). Error bars indicate standard deviation across triplicate datasets.

doi: https://doi.org/10.1371/journal.pcbi.1014102.g003