Extended Data Fig. 5: Stanford and NeoTRIP cohort overview.

(a-g) Stanford cohort. (a) Pie chart shows the number of patients that did (pink) or did not relapse (blue). (b) Histogram shows the number of cells in each tumor image. (c) Heatmap shows the average standardized expression of twenty cell phenotypes clustered according to protein expression of phenotypic markers. Barplots to the right show the total number of cells within each cell phenotype. (d) Barplots show the frequency of tumor (top), structural (middle) and immune lineages (bottom) across all primary tumor samples in this cohort. Samples were hierarchically clustered according all frequency subsets. Relapse status is denoted by color in the top row. (e) Violin plots show the top 15 differentially-enriched niche neighborhoods in patients who relapsed (red) or did not relapse (blue). Barplots to the right show the proportion of patients with a niche neighborhood in the respective patient groups. (f) Niche network for non-relapsing patients, where nodes represent cell types within recurrence-free niches and edge weights correspond to the number of unique patients with the corresponding interaction. Node size is proportional to connectedness, as measured by eigenvector centrality. (g) Niche network for relapsing patients, where nodes represent cell types within recurrence-associated niches and edge weights correspond to the number of unique patients with the corresponding interaction. Node size is proportional to connectedness, as measured by eigenvector centrality. (h-n) NeoTRIP cohort analysis, where pCR is complete pathologic response and RD is residual disease. Source data is provided in the Source Data file.