Fig. 5

Single-cell proteomes define a continuum of macrophage polarization states. a Heatmap of the top 20% most variable proteins (609) between two clusters of cells identified by unsupervised spectral clustering of all quantified proteins and cells. The cells are ordered based on their rank in the corresponding Fiedler vector from the spectral clustering, see Eq. 1. The color bars above the heatmap indicate the loadings of each cell in the Fiedler vector. b Gene set enrichment [37] identified overrepresented functions for the proteins enriched within each cell type. These functions are displayed alongside representative protein distributions from each gene set. c The unsupervised spectral analysis from panel a was applied only to the macrophage-like cells, revealing a gradient of macrophage heterogeneity. Cells were ordered based on the corresponding elements of the Fiedler vector, Eq. 1. The bars above the heatmap indicate the Fiedler vector loading of each cell. The top 25% of proteins with the largest fold change between the first 40 cells and last 40 cells are displayed (761 proteins). The single-cell levels of genes in the protein data set previously reported to be enriched in M1 or M2 polarized primary human macrophages [38] are displayed at the bottom; each data point represents the median value over bins of 110 cells (1096 macrophage-like cells total), and error bars denote standard error of data points in each bin