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Fig. 1 | Genome Biology

Fig. 1

From: MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

Fig. 1

Metacell analysis of the PBMC 8K dataset. a Schematics of the MC algorithmic pipeline. b Outlier/rare cells matrix showing color-coded number of UMIs per cells (columns) for which at least one gene (rows) was shown to be expressed significantly beyond its MC expected number of UMIs. Outlier/rare cells are ordered according to the annotation of the MC containing them (bottom color-coded bars). c Shown are log-fold-enrichment (lfp, methods) values for metacells, color-coded according to initial cell type annotation, comparing the T cell marker (CD3D) to a B cell (CD79A) and myeloid (LYZ) markers. d Heat map shows enrichment values for metacells (columns) and their maximally enriched gene markers. e Shown is the MC adjacency graph (numbered nodes connected by edges), color-coded according to their cell type and transcriptional state annotation. Cells are shown as small color-coded points localized according to the coordinates of MCs adjacent to them. Additional file 2: Figure S3 shows the adjacency matrix that was used to generate the projection

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