Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference
Fig 5
Different quality metrics confirm consistent preservation of the algal microbiome pattern with F-informed MDS.
Seven dimension reduction methods were evaluated for their preservation of (A) local and (B) global structure by calculating trustworthiness and continuity using two nearest neighbor numbers k = 3 (local), k = 27 (global). The methods were also assessed based on (C) global distortion metrics (Stress-1 and Shepard plot correlation) and (D) the ratio of p-values (F-rank-ratio) and correlation in F-ratios (F-correlation) using randomly permuted label set. A dataset of N = 36 bacterial communities was analyzed as described in section “Real microbiome community” of Methods. The following hyperparameters were applied: (F-MDS), number of neighbors nU (UMAP, supervised (-S) and unsupervised (-U)), perplexity “perp” (t-SNE), and the number of shortest dissimilarities nI (Isomap).