Extended Data Fig. 1: Prevalence of foreign cell type markers in scRNA-seq data compared to spatial, after adjusting for modality-specific differences.

a, To demonstrate that the spatial modality has more admixing compared to scRNA-seq, we computed the expression of malignant marker genes in each cell type. The bar height shows the total expression of select malignant marker genes after correcting for modality-specific expression differences of these markers as identified in the malignant cell type. This is calculated by first computing the mean fractional expression of each marker in each cell type. Expression for a marker is normalized by its ratio of spatial to scRNA expression in malignant cells, and these values are summed over all markers (making the first two bars equal height). b, As with a but for admixture of enterocyte markers into other cell types in the mouse ileum datasets.