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Create UMAP embeddings from SNN graph

Source: R/hc_umap.R
hc_umap.Rd

hc_umap() generates UMAP embeddings based on the Shared Nearest Neighbors (SNN) graph stored in the AnnDatR object.

Usage

hc_umap(AnnDatR, n_epochs = NULL, seed = 42, verbose = TRUE)

Arguments

AnnDatR

An AnnDatR object containing the data with SNN graph results.

n_epochs

Number of epochs for UMAP optimization. If NULL, it will be set to 200 for datasets with more than 10,000 cells and 500 otherwise (default is NULL).

seed

Random seed for reproducibility (default is 42).

verbose

Logical indicating whether to print progress messages (default is TRUE).

Value

UMAP embeddings stored within the AnnDatR object.

Examples

# Generate UMAP embeddings on an AnnDatR object after SNN graph computation
adata_res <- hc_pca(example_adata, components = 40)
adata_res <- hc_distance(adata_res, components = 20)
adata_res <- hc_snn(adata_res, neighbors = 15)
#> Building SNN based on a provided distance matrix
#> Computing SNN
adata_res <- hc_umap(adata_res)
head(adata_res$obsm$X_umap)
#>                     UMAP_1     UMAP_2
#> ENSG00000002745 -0.9571011 0.44796989
#> ENSG00000004660 -0.2335736 0.05524627
#> ENSG00000006047  0.9501483 0.06922970
#> ENSG00000006059 -0.5981353 0.53429342
#> ENSG00000006453 -0.4365061 0.43445204
#> ENSG00000006740 -0.2108534 0.07438501