Extended Data Fig. 5: Differential abundance analysis between IMNM versus IBM and CTRL versus IMNM. | Nature Aging

Extended Data Fig. 5: Differential abundance analysis between IMNM versus IBM and CTRL versus IMNM.

From: Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis

Extended Data Fig. 5

a Top: Neighborhood graph visualizing results of differential abundance analysis (DAA) between IMNM and IBM in myonuclei. Bottom: Beeswarm plot showing log(fold-changes) (log(FC)) of abundances in neighborhoods between IMNM and IBM in myonuclei. b Top: Neighborhood graph visualizing results of DAA between IMNM and IBM in immune cells. Bottom: Beeswarm plot showing log(FC) of abundances in neighborhoods between IMNM and IBM in immune cells. c Top: Neighborhood graph visualizing results of DAA between IMNM and IBM in endothelial-stromal cells. Bottom: Beeswarm plot showing log(FC) of abundances in neighborhoods between IMNM and IBM in endothelial-stromal cells. d Top: Neighborhood graph visualizing results of DAA between CTRL and IMNM in myonuclei. Bottom: Beeswarm plot showing log(FC) of abundances in neighborhoods between CTRL and IMNM in myonuclei. e Neighborhood graph visualizing results of DAA between CTRL and IMNM in immune cells. f Top: Neighborhood graph visualizing results of DAA between CTRL and IMNM in endothelial-stromal cells. Bottom: Beeswarm plot showing log(FC) of abundances in neighborhoods between CTRL and IMNM in endothelial-stromal cells. g Heatmap visualizing average expression of selected marker genes of Group6. For neighborhood graphs in a - f: Nodes represent neighborhoods, colored by log(FC) between IMNM (red) and IBM (blue) (a – c) or CTRL (red) and IMNM (blue) (d - f). Neighborhoods with no detected differential abundance (corrected spatialFDR > 0.1) are colored white (a - f). Node size correlates to the numbers of nuclei within a neighborhood (Nhood size) and graph edge width indicates the number of overlapping cells between adjacent neighborhoods (overlap size). Node positions are based on positions of nuclei as shown in Fig. 2a, d, g. For beeswarm plots in a – d, and f: Every dot represents a neighborhood, colored by log(FC) between IMNM (red) and IBM (blue) (a – c) or CTRL (red) and IMNM (blue) (d and f). Neighborhoods with no detected differential abundance (corrected spatialFDR > 0.1) are colored grey. ‘Mixed’ indicates < 70% of nuclei within a neighborhood originate from one cluster.

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