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Compute distance matrix from PCA scores

Source: R/hc_distance.R
hc_distance.Rd

hc_distance() computes a distance matrix based on PCA scores stored in the AnnDatR object.

Usage

hc_distance(AnnDatR, components = NULL, method = "spearman")

Arguments

AnnDatR

An AnnDatR object containing the data with PCA results.

components

Number of principal components to be used. If NULL, it will be set to the first component with over 80% explained variance.

method

Distance metric to use (default is 'spearman'). This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski", "pearson", "spearman" or "kendall".

Value

Distance matrix stored within the AnnDatR object.

Examples

# Compute distance matrix on an AnnDatR object after PCA
adata_res <- hc_pca(example_adata, components = 40)
adata_res <- hc_distance(adata_res, components = 20)
head(adata_res$uns$distance)
#> [1] 0.8857143 1.3804511 1.0812030 0.9609023 1.2120301 1.2451128