(a) A heatmap showing the hallmark genes expressed by various T cell subsets in the BALFs. (b) The bar plot shows the fraction of cells in each T cell subset for which both transcriptomes and TCR clonotypes data can be characterized. (c) The bar plots show the individual top 20 expanded T cell clones (each bar represents a single T cell clone) in the BALFs of moderate (upper panel) and severe/critical (lower panel) COVID-19 patients. The 20 clones were aligned from left to right according to their cell numbers in each clone. The colored segments of the bar indicating which subsets the cells of that clone belong to. (d) The volcano plot shows the selected DEGs of expanded vs. non-expanded CD8+ T cells in BALFs of moderate COVID-19 cases (n = 3). A gene is considered significant with adjust P < 0.05 (P-value adjusted by false discovery rate in MAST). Other indicates non-significant genes.