total_distance: Calculates the total distance between groups in seurat object

Description Usage Arguments Value See Also

View source: R/distance.R

Description

Calculates the distance between the every point in both clusters. Including within their own clusters.

Usage

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total_distance(seurat_object, group, reduction = "pca", dims = 1:30,
  distance = "euclidian", output = "seurat", method = "all")

Arguments

seurat_object

A seurat object

group

Seurat Categories or groups for which the distances between are calculated. Cell wise data.

reduction

Dimensionality reduction data to use

dims

Which dimensions to use

distance

Point to point distance to use. Options are "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"

output

Output type. Default is "seurat". Options are "seurat" (Seurat S4 object), "list" (List of tables by split_by), "seurat_list" (List of Seurat objects). Seurat objects returned have the distance data stored internally.

method

The number of cells in group 1 to test. This is done because calculating the total distance is often very computationally expensive. And by reducing the number of cells in group one can give an approximation of the final result without having to test all cells. Options are "one" ( calculate for one cell in group 1), "all" (calculate for all cells)

Value

List containing distances between groups per row

See Also

Other total_distance: PlotTotalDistance, total_linkage


sbrn3/disscat documentation built on Dec. 12, 2019, 7:54 a.m.