Extended Data Fig. 5: LYVE1^hiMHCII^low macrophages get activated in PAD.

a, Dot plot of logcount values of markers from different myeloid populations in Monocytes/Macrophages subtypes. Color and size of the dots indicate the logcount value and the proportion of cells that express the gene, respectively. b, Dot plots of logcounts values of LYVE1, CX3CR1 and MHC-II class genes in LYVE1^hiMHCII^low and LYVE1^lowMHCII^hi macrophages. Color and size of the dots indicate the logcount value and the proportion of cells that express the gene, respectively. c, Stacked bar plots showing cluster percentage in each condition in the spatial dataset from non-ischemic (n = 3) and PAD (n = 3) patients, color-coded by cluster. Each stack represents mean - SEM. d, Heatmap of centered values from ORA analysis over the DEGs in cMonocytes between conditions, color indicates the centered values. The left heatmap shows all identified enriched processes, while the right heatmap only shows terms related to leukocyte/myeloid cell/macrophage differentiation. e, Heatmap of logcounts values of DEGs (adjusted p-value < 0.05) between LYVE1^hiMHCII^low macrophages in non-ischemic and PAD, color indicates the logcount value. f-g, Heatmap of centered values from ORA analysis over the DEGs in LYVE1^hiMHCII^low macrophages between conditions, color indicates the centered values. Panel f displays all the enriched processes and panel g focuses on top enriched processes in each condition. Wilcoxon Rank Sum test (as implemented in Seurat package) was used in e.

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