Fig. 1

Atlas of immune cells and stromal cells in the gastric cancer TME before and after NACT. A–C t-SNE plots of all immune cells and stromal cells with each cell color coded for the patient ID (A), cell type (B), and before and after NACT (C). D Dot plot annotating the major cell types based on the cell markers in all samples. The circle size indicates the cell fraction expressing the signature at a level greater than the mean; the color indicates the mean signature expression (red, high; blue, low). E Fractions of different cell types in the total cell population in pretreatment (n = 7) versus post-treatment (n = 7) samples. Unpaired t test was performed to compare pretreatment and post-treatment samples. P value was shown if there was a significant difference. n.s.: not significant