Fig. 8
From: mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis
Analysis of oral microbiomes of chronic periodontitis. a Data ordination and beta diversity analysis between CP patients and healthy controls, with tongue samples removed. b Data ordination and beta diversity analysis between subg and supra sites. Included were algorithm-based (PCA and t-SNE), model-based (ZIFA, PPCA-NB, mbDenoise-zinb), and denoising methods (PPCA-NB, mbDenoise-zinb and SAVER) by applying PCA and t-SNE to the denoised data. Inputs of PCA and t-SNE were log-transformed. Beta diversity was assessed using PERMANOVA