Fig. 1

a t-SNE projections of scRNA-Seq profiles for each tumor colored by unsupervised clustering resulting from Phenograph analysis. We note that while the putatively transformed populations in each tumor appear in red for simplicity, the majority of them actually contain multiple Phenograph clusters as shown in d and detailed in Fig. 3. The cell type labels are based on marker expression patterns shown in Additional file 1: Figures S2–9. b Principal component analysis of the z-scored matrix of average chromosomal expression for each tumor showing a characteristic axis of variation, which we call the “malignancy score”, on which the putatively transformed cells are separated from the untransformed cells in each tumor. c Same as a but colored based on the malignancy score in b. d Distributions of malignancy scores for each Phenograph cluster in a showing that all of the putatively transformed clusters have higher median scores than all of the untransformed clusters within each tumor. Stars indicate the putatively transformed clusters. e Heatmaps showing the average copy number of each chromosome based on low-pass, bulk WGS (top) and heatmaps showing the average expression of each chromosome in each cell associated with a transformed cluster relative to the average untransformed cell in each tumor (bottom). The high resolution version of Figure 1 is also available as Additional file 2