CytoPy: An autonomous cytometry analysis framework
Fig 4
Batch correction using the Harmony algorithm.
(A) Single cell UMAP plots are coloured by cell origin, where each colour represents a unique patient. Shift in batch membership in the local neighbourhood of cells is shown by the change in the UMAP plot after Harmony is applied and by the shift in LISI distribution. (B) Cell population structure is conserved after correction as shown by the shape of latent variables UMAP1 and UMAP2, and the distribution of the cell surface markers CD4, CD8, the linear combination of p Pan-γδ and Vδ2 (to identify Vδ2+ γδ T cells), and the linear combination of CD161 and Vɑ7.2 (to identify MAIT cells).