Figure 3.
Focal infiltration of immune cells in EMD lesions. (A) Clusters generated using the Leiden algorithm based on estimated cell type abundances calculated from cell type deconvolution using cell2location of ST data of samples taken from PT01A, PT01B, PT03, and PT11 for T-cell–infiltrated lesions and PT02 and PT09 for T-cell depleted lesions. (B) Heat map showing the scaled z score of estimated cell abundance of cell types across Leiden clusters shown in panel A for T-cell–infiltrated lesions (PT01A, PT01B, PT03, and PT11). (C) Estimated spatial cell type abundances of PCs, T-cells Tim3+, M1 macrophages, and CD8+ cytotoxic T cells across samples, as in panel B.

Focal infiltration of immune cells in EMD lesions. (A) Clusters generated using the Leiden algorithm based on estimated cell type abundances calculated from cell type deconvolution using cell2location of ST data of samples taken from PT01A, PT01B, PT03, and PT11 for T-cell–infiltrated lesions and PT02 and PT09 for T-cell depleted lesions. (B) Heat map showing the scaled z score of estimated cell abundance of cell types across Leiden clusters shown in panel A for T-cell–infiltrated lesions (PT01A, PT01B, PT03, and PT11). (C) Estimated spatial cell type abundances of PCs, T-cells Tim3+, M1 macrophages, and CD8+ cytotoxic T cells across samples, as in panel B.

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