Fig. 4

Recluster of T/NK cells and overview of TCR distribution across different groups. A. TSNE plot of 11,847 T/NK cells reclustered, colored according to cell subtypes (Top), colored according to TCR detected (Bottom). Each dot represents a single cell. B. Dot plot of functional genes expression in each T/NK subclusters. C. Canonical markers expression for each T/NK subclusters. D. Percentage of each T/NK subtypes in different groups. Error bars represent mean ± SEM. Colored dots represent different samples. Differences with p < 0.05 were indicated; two-sided unpaired Wilcoxon rank sum test was used for comparison. E. LOESS fitting plot showed the correlation between the number of T cell clones and the number of cells per clonotype. Solid line is used to display the correlation, and dashed line is used to separate between nonclonal and clonal cells. F. Status of immune repertoire space occupancy of clones across different groups by stacked bar chart. The occupancy of the clone space was analyzed by sorting all clonotypes in descending order based on their frequency of occurrence. The data were then separated into different bins using cutoff values of 10, 100, 1000, and 10,000, and stacked bar chart was then plotted to visualize the distribution of clonotypes among the different bins. G. The percentage of clones with different frequencies across different groups. H. Status of TRA/B genes usage across different groups. The colors indicate the usage percentage of specific V-J gene pairs. Abbreviation: LOESS: Locally Weighted Scatterplot Smoothing; SEM: Standard error of mean; TCR: T cell repertoire