Extended Data Fig. 4: Analysis of scRNA-seq data by unbiased clustering.
From: Mapping the T cell repertoire to a complex gut bacterial community
a, Uniform manifold approximation and projection (UMAP) plot of all the cells. The data is generated by merging three groups: hCom1d-colonized, hCom2d-colonized, and germ-free mice. Cells were clustered into 25 groups using the FindClusters function of the Seurat R package. b–d, Gene expression profiling of cell clusters. To investigate the identity of each cell cluster, expression levels of cell subset markers were visualized by dot plots (b), feature plots (c) and violin plots (d) using Seurat.
