Fig. 4

Identifying cell clusters by principal component analysis and evaluating SCoPE2 quantification. a A weighted principal component analysis (PCA) of 1490 single cells using all 3042 proteins quantified across multiple single cells. Missing values were imputed using k-nearest neighbor (k = 3). Cells are colored by cell type. b The cells from the PCA in a are color-coded based on the abundance of monocyte and macrophage genes, defined as the 30 most differential proteins between bulk samples of monocytes and macrophages. c The relative protein levels (macrophage/monocyte protein ratios) estimated from the single cells correlate to the corresponding estimates from bulk samples; ρ denotes Pearson correlation. Proteins functioning in signaling (d) as well as the least abundant proteins quantified by SCoPE2 (e) allow clustering cells by cell type. The protein fold changes between monocytes and macrophages for these protein sets are consistent between single cells and bulk samples, similar to c