Extended Data Fig. 3: NMF and cell subset ranking.
From: Cross-tissue multicellular coordination and its rewiring in cancer
(a) NMF rank selection based on cophenetic correlation coefficients and their consistency, with the final rank chosen as 12 (Methods). (b) Consensus plot for NMF with a rank of 12. (c) Bar plots showing the top 15 cell subsets ranked by NMF weights for each factor (CM). (d) Topological and statistical evaluations of CMs, with the connectivity score defined as the ratio of observed edges to the total possible edges among all nodes within the CM network. (e) CM activities in scRNA-seq samples across 34 tissues. Each sample is assigned a CMT based on its dominant CM, with samples ordered by CMT identities and tissues. (f) CM Shannon equitability across tissues. For box plot in d, the center line represents the median, the box limits delineate the upper and lower quartiles, and the whiskers extend to the highest and lowest values within 1.5× the interquartile range.
