Fig. 2

Subcellular localization pattern identification with RNAforest. A Thirteen spatial summary statistics are computed for every gene-cell pair describing the spatial arrangement of molecules and boundaries in relation to one another. The features (Supp. Table 1) are inputs for RNAforest, a multilabel ensemble classifier that assigns one or more subcellular localization labels: cell edge, cytoplasmic, nuclear, nuclear edge, and none. The colors for each label are used consistently throughout to figure. Top 10 genes for each label visualized for each label other than “none” in B U2-OS cells and C 3T3 cells. D and E are UpSet plots showing the proportion of measured transcripts assigned to each label. F and G show the relative label proportion across cells for each gene and are colored by the majority label (F and G). H Top 5 consistent genes for each label. I ssGEA identifies the enrichment of GO cellular component domains for each label in the 3T3 cell dataset. Stars denote p-values under thresholds defined in the legend. P-values are derived from ssGSEA permutation tests with Benjamini–Hochberg correction controlling for false discovery rate