Extended Data Fig. 7: Detection of profibrotic (SPP1hi) macrophages with alternative reference designs.

(a) Scatterplots of differential abundance log-Fold Change (DA logFC) against the mean expression of profibrotic macrophage signature in macrophage cell neighbourhoods with ACR design (left), AR design (middle) and CR design (right). Coloured points indicate neighbourhoods where the enrichment was significant (1% SpatialFDR and logFC > 0). Pearson’s correlation coefficients and p-values for significance of the correlation are reported (two-sided test). (b) Analysis of top 10% macrophage neighbourhoods prioritized by DA logFC using ACR and CR designs. When examining prioritized neighbourhoods with low expression of profibrotic signature (top 10% false positives), we found that with the CR design these neighbourhoods include cells from significantly less samples compared to the true positives. On the left, we mark neighbourhoods that are considered top 10% (colored), separating out False Positive (FP) neighbourhoods, where the mean profibrotic macrophage signature was below the threshold of the 90% quantile used for precision-recall analysis. The boxplots on the right show the number of samples represented in each top 10% neighbourhood (ACR other: n = 10 neighbourhoods; ACR FP: n = 65 neighbourhoods; CR other: n = 66 neighbourhoods; CR FP: n = 18 neighbourhoods). In boxplots the center line denotes the median; box limits, first and third quartiles; whiskers, 1.5X interquartile range. (c) Barplots of fraction of cells from each donor in top 10% false positive neighbourhoods with ACR (left) and CR design (right). (d) Detection of profibrotic macrophages with label transfer uncertainty score from Sikkema et al. 2022. Violin plots show the distribution of label uncertainty on cells (left), mean label uncertainty on neighbourhoods (centre) and DA logFC with ACR design for profibrotic macrophages (profibrotic macrophage signature > 90% quantile, in pink) and other macrophages (in grey). The dotted lines denote the median value and inter-quartile range. (e) Precision-recall curve for detection of profibrotic macrophages with metrics shown in D. The dotted lines denote the baseline value for the AUPRC, indicating the case of a random classifier.