Non-linear archetypal analysis of single-cell RNA-seq data by deep autoencoders
Fig 7
scAAnet identified 3 GEPs in the lung fibroblast and myofibroblast cells.
(a) The UMAP visualization (Methods) of observed scRNA-seq data colored by cell types. (b) The UMAP visualization of observed scRNA-seq data colored by disease groups. Black dots in a and b are locations of cells that have the largest usage of the corresponding GEP (marked in Arabic numerals). (c) UMAPs colored by inferred cell usage for each GEP. (d) Heatmap showing the usage of all GEPs (rows) in all cells (columns). Cells are ordered by hierarchical clustering. (e) Heatmap showing the percentage of cells with usage > 25% of each GEP (rows) in each cell type and disease group (columns). Colors of cell types and disease groups in d and e are coded in the same way as colors in a and b. (f) Box and whisker plot of the usage of each GEP in cells of fibroblast (top) and myofibroblast (bottom), colored by disease groups (colors are coded in the same way as in b). Central lines represent medians, boxes represent the IQR, and whiskers represent the 5th and 95th quantiles.