Extended Data Fig. 2: Control analysis for purity of single-cell RNA-Seq data. | Nature Genetics

Extended Data Fig. 2: Control analysis for purity of single-cell RNA-Seq data.

From: Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

Extended Data Fig. 2: Control analysis for purity of single-cell RNA-Seq data.

a. UMAP embeddings of cells annotated as malignant per cancer type or organ system, colored by sample. b. Control analysis for annotations of cells as malignant, using the method described by Kim et al.1. Briefly, inferred CNV profiles (from the scRNA-Seq data) were scored as the sum of the squared values (shown as the x-axis). The cells with the top 10 scores are assumed to be malignant and each cell is then correlated with the average profile of the top 10 cells (y-axis). In tumors with CNVs these two measures are consistent. Color indicates the annotation as malignant or normal cells, per sample.

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