Fig. 4

Smoother detects tumor-specific plasma cell subtypes in colorectal adenocarcinoma Stereo-seq slide. a UMAP representation of the cell types from the patient-derived paired colorectal adenocarcinoma scRNA-seq reference [18]. b Expression dot plot of the top marker genes for each cell type in the scRNA-seq samples. c Pathology annotation of the histology slide, adapted from [18]. d Slide subregions identified by clustering based on estimated cell-type compositions. Arrows emphasize the mucosa delineation apparent with Smoother but not CARD. e Spatial visualizations of the cell-type proportions of the three plasma cell subtypes. f B-cell receptor gene expression heatmap for the IgA plasma cell spots in the mucosa and the IgG plasma cell voxels in the lesion, normalized across spots. g Gene Ontology pathway enrichment analysis of the IgA plasma cell and IgG plasma cell spots. h Colocalization of each cell type with the IgA and IgG plasma cells. Statistical significance is calculated by comparing the inferred proportions of a given cell type at IgA-specific spots with proportions at IgG-specific spots using the Wilcoxon test