FIG. 4.

(A) Two TME topics found near the tumor-immune boundary. Topic 2 corresponds to the TME cluster reported in Keren et al. (2018), whereas topic 1 is a new, immunosuppressive topic. Red points denote tumor cells where intensity denotes the degree to which a tumor cell's microenvironment resembles a given topic. Gray points denote immune cells. (B) Topics discovered by spatial LDA and their preferences for cells expressing different markers. Red entries denote a strong preference for cells expressing that marker and blue relatively low preference. TME, tumor immune microenvironment.