The specious art of single-cell genomics
Fig 2
Distortion of necessary properties in embeddings.
(a) (i) Distribution of Jaccard distance of cell neighbors in PCA-preprocessed 2D embeddings and the relevant PCA space, as compared to ambient space. (ii) Distribution of Jaccard distance of cell neighbors in PCA-preprocessed 2D embeddings, as compared to the higher dimensional PCA space. (b) (i) Boxplot of correlations of cell type neighbor rankings to ambient space for the PCA-preprocessed 2D embeddings and the relevant PCA space. (ii) Boxplot of correlations of cell type neighbor rankings to the relevant higher dimensional PCA space for the PCA-preprocessed 2D embeddings. Embeddings generated n = 3 times. (c) Selection of equidistant groups with “near” or “far” distances in ambient space. UMAP embedding of the data in gray circles, with orange circles denoting all cells within the previously determined equidistant groups.