Fig. 4

a (zebrafish embryo) Wnt and BMP signalings interpolated from the SpaOTsc cell–cell communication matrix and mapped to space using the mapping between cells and positions. The arrow lengths indicate the signal sending probability of the position and the color shows the estimated signal receiver probability distribution over space. The scRNA-seq data from ref. ³⁶ and spatial data from ref. ¹³ were used. b (zebrafish embryo) Wnt and BMP signaling summarized into cell clusters. c, d (Drosophila embryo) Spatial ranges of Wg and Dpp signaling inferred using a series of sets of random forest models. The gray band represents the 95% confidence interval. The experiment was repeated three time with similar results. e (Drosophila embryo) Left: cell–cell communications of Wg signaling at the single-cell level using a visualization (UMAP) constrained by cell–cell distance. The color of the link is marked by the color of the sending cells, based on the clustering using only scRNA-seq data. Right: cluster–cluster communications of Wg signaling based on SpaOTsc spatial subclustering (subcluster the previously determined clusters based only on scRNA-seq data using the cell–cell distance). f (Drosophila embryo) Dpp signaling in space plotted similar to (e).