CytoPy: An autonomous cytometry analysis framework
Fig 2
UMAP plots revealing batch effect in T cell staining of whole blood.
A reference sample (blue) is chosen as the ‘average’ sample in Euclidean space. A low dimension embedding of this sample is made using UMAP (other algorithms are available in CytoPy, e.g. PCA, PHATE, t-SNE) and samples for comparison are projected into this same space (red), demonstrating ‘drift’ in cell populations between patient samples. Each plot depicts results obtained with cells from an individual patient; numbers shown are unique patient sample identifiers.