Fig. 4: ELVAR predicts increased stem-cell and T-regulatory cell fractions in polyps.

a Top panel: The cell-cell similarity graph inferred using Seurat on scRNA-Seq data with epithelial enterocyte lineage cells annotated by community membership, as inferred using ELVAR. Middle and lower panels depict the same graph but with cells annotated by disease stage (N = normal, U = unaffected, P = polyp, A = adenoma) and cell-state. Data is shown for one representative ELVAR run. b Alluvial plot displaying composition of ELVAR communities according to disease stage and cell-state. c As a but for lymphocyte-cells in colon tissue. d As b but for the lymphocyte cells in colon-tissue. e Boxplots displaying the stem-cell (left panel) and T-regulatory cell (right panel) fraction as a function of disease stage, considering only cells that are part of significantly enriched ELVAR-clusters. P-value derives from a two-sided linear regression. Boxplot elements indicate median, interquartile range (IQR) and whiskers extend to 1.5 times the IQR. f Violin plots comparing ELVAR to the analogous DA-testing algorithm that uses non-sequential Louvain in place of EVA (“LVnonseq”). The y-axis labels the corresponding z-statistics from negative binomial regressions (100 runs each) of stem-cell or T-regulatory cell counts against disease stage. Gray dashed line indicates the P = 0.05 significance level. P-values shown derive from a one-tailed Wilcoxon rank sum test comparing the ELVAR z-statistic distribution to the one derived using “LVnonseq”. Source data are provided as a Source Data file.