eucldist

Computes pairwise Euclidean distances between group centroids (mean embedding vectors) in a specified low-dimensional representation of a Seurat object.

Usage

.eucldist(seurat_object, groupby, reduction, verbose = TRUE)

Arguments

seurat_object

A Seurat object.

groupby

A character scalar giving the name of a metadata column in seurat_object@meta.data that defines group labels.

reduction

A character scalar giving the name of a dimensional reduction (e.g., "pca", "harmony") used for distance calculations. This should be a geometry-preserving representation; visualization-oriented nonlinear embeddings (e.g., "umap", "tsne") are not recommended for distance computation.

verbose

Logical; if TRUE, prints progress messages.

Value

A symmetric data.frame (groups \(\times\) groups) of Euclidean distances between group centroids.

Details

For each group defined by groupby, the centroid is computed as the column-wise mean of cell embeddings in reduction. Euclidean distances are then computed between all pairs of group centroids.