Fig. 4

RNAflux finds distinct subcellular domains with consistent spatial organization and local gene composition. A Flowchart of RNAflux and fluxmap computation. Local neighborhoods of a fixed radius are arrayed across a cell and a normalized gene composition is computed for each pixel coordinate, producing an RNAflux embedding. The first three principal components of the RNAflux embedding are visualized for U2-OS cells coloring RGB values by PC1, PC2, and PC3 values respectively for each pixel. Fluxmap domains are computed from each RNAflux embedding to create semantic segmentation masks of each subcellular domain. B The left panel shows a field of view of U2-OS cells, dots denoting individual molecules colored by gene species, nuclei, and cell boundaries outlined in white. For the same field of view of cells, the center panel shows RNAflux embeddings and the right panel shows fluxmap domains. C The scatter plot shows how the composition of each gene is distributed across fluxmap domains. The position of each point denotes the relative bias of a given gene’s composition across fluxmaps. D Heatmap showing the fraction of pixels with a positive enrichment value for each APEX-seq location for each fluxmap domain. E–I The most highly enriched location is shown for each fluxmap domain. Domain boundaries are denoted by white lines within each cell