Fig. 4

Analytic pipeline and results summary for two tissues from the HER2 + BRCA 10 × Visium dataset. A The analytic pipeline built on the SRT-Server. The constructed analytic pipeline uses seven analytic modules, with the parameter settings for each module visualized on the panel. B The H&E staining image displays the general tissue structure. C A spatial scatter pie plot displays the inferred cell-type compositions across spatial locations from CARD in the DECON module. D 10 detected spatial domains from SpatialPCA in the SDD module. We used the clustering result in domain number = 10 to all the downstream analysis, which is not mentioned in the pipeline. E The pseudo-time inference result in the cancer epithelial is obtained from slingshot in the TRAJ module after DECON analysis. F The pseudo-time inference results are obtained from slingshot in the TRAJ module. The left two panels show the pseudo-time of different cell types on the two samples. The right two plots include arrows to display pseudo-time change on the tissue: the arrow point from tissue locations with low pseudo-time towards tissue locations with high pseudo-time