Fig. 3: Complementary spatial niche analyses provide comprehensive annotation of tissue remodeling in PF.

a, Representative examples from both unaffected and PF samples showing transcript- (left) and cell-based niches (right). VUHD113 and VUILD107MA (IPF diagnosis) are shown. For transcript niches, hexbin plots are shown (Methods). For cell niches, each point is a cell centroid. b, Cell assignment to transcript- (top) and cell-based niches (bottom), as a proportion of the number of cells of each type (each column sums to 1; columns indicated by gray lines). c, Bar plots depicting the total proportion of cells across the unaffected, less affected and more affected sample types assigned to each transcript and cell niche. d, The niche composition of select annotations, as a proportion of the number of cells across an annotation (each row sums to 1; rows indicated by gray lines). For b and d, proportions under 0.01 are not shown, and the proportion legend applies to both panels. See Supplementary Fig. 17b for expanded version (d) with all annotations listed. Different colors in c indicate niche colors for all panels. Micro., microscopic; Min., minimally.