Fig. 4: Stereopy enables temporal analysis of spatial transcriptomes with multiple samples.

a Graphical abstract depicting the pipeline for time series analysis. b Spatial trajectory visualization of mouse embryo multi-sample transcriptomes from E9.5 to E16.5. c Tree plot indicating the development of mouse embryo ectoderm. The x-axis represents time point, the dot size represents the cell number, and the red arrow indicates the PAGA trajectory. d Manual annotation and pseudotime assignment for time-series mouse brain samples. e Development tree for cell types in the time series. The x-axis represents time point, and the height of Sankey represents the cell number of a certain cell type at a particular time point. f PAGA graph for mouse brain trajectory inference. Red arrow points at the cell types selected for downstream analysis. g Up and downregulated genes for the mouse forebrain trajectory and GO enrichment analysis. The cell numbers for each cell type are 3972, 524, 2827, 2838, 3629, respectively. The box extends from the first quartile (Q1) to the third quartile (Q3) and the line inside represents the median. The whiskers extend from the box to the farthest data point lying within 1.5 times the inter-quartile range from the box. Flier points are those beyond the end of the whiskers. h F-score among time points and correlation with pseudotime of the top 1000 gene for each cluster using Stereopy-TGPI (blue) and Mfuzz (yellow) methods. i A temporal gene pattern identified by Stereopy-TGPI for mouse forebrain trajectory. j A temporal gene pattern identified by Stereopy-TGPI for mouse forebrain time series datasets. The upper and lower edges of the error band represent Q1 and Q3 of the gene expression levels of the gene group in i and j, respectively. k Gene expression of Tead1 in each cell type at each time point. l Spatial heatmap for AUC scores of Tead1(+) regulons and corresponding GO terms. m Time-series gene network for Tead1. The radial line represents a group of genes, and the points on it indicate the time points when these genes are expressed. The point size indicates the gene number. Source data are provided as a Source Data file.