Extended Data Fig. 2: Identification and comparison of cNMF programs in peripheral myeloid cells to tumor programs.

a) cNMF programs identified from scRNA-seq profiles of peripheral blood from glioma patients. Plot compares cNMF programs between peripheral myeloid cells and glioma-associated myeloid cells. Heat and dot size correspond to Jaccard Index between gene spectra. b) For each myeloid cell type, stacked bar shows the absolute number of cells with top usage of indicated activity programs. c) For each myeloid cell type (rows), horizontal bars indicate the percent of cells with >20% usage of the indicated activity program. d) Heatmap shows relative enrichment of the indicated activity programs (columns) across the different cell identities (rows). P value calculated using hypergeometric distribution. e) Schematics depicts expansion of the cohort to include the McGill samples in all subsequent analyses. f) Violin plots shows the usage of each immunomodulatory program in cells with >20% usage of the Scavenger Immunosuppressive program (left) or the Complement Immunosuppressive program (right). g) Quadrant plots position cells (dots) by their expression of the immunomodulatory programs as in Fig. 1e. Grayscale depicts usage of the indicated immunomodulatory program. The position of each dot represents the difference in the usage of immunosuppressive and inflammatory programs by that cell (the upper part of the plot is more inflammatory, while the lower part is more immunosuppressive). h) Quadrant plot as in g but with cells colored by cohort. Overall, the four immunomodulatory programs are shared across myeloid cell types, but are rarely utilized by the same cells. PBMC tube, Shalek, A. (2005) https://BioRender.com/b15i535.