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Plot UMAP with clusters and hulls

Source: R/hc_plot_umap.R
hc_plot_umap.Rd

hc_plot_umap() creates a UMAP plot from an AnnData object, displaying points, cluster hulls, or both.

Usage

hc_plot_umap(AnnDatR, plot = c("points", "hulls", "both"))

Arguments

AnnDatR

An AnnData object containing UMAP coordinates and cluster hulls.

plot

Type of plot to create: "points" for scatter plot, "hulls" for cluster hulls, or "both" for overlaying points on hulls. Default is "points".

Value

A ggplot2 object representing the UMAP visualization.

Examples

# Plot UMAP points from an AnnDatR object
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_cluster_consensus(adata_res, resolution = 7)
#> Iteration: 0 *** value: 948.279
#> Iteration: 1 *** value: 70.5063
#> Iteration: 2 *** value: 22.246
#> Iteration: 3 *** value: 22.2447
#> Iteration: 4 *** value: 22.2447
#> Minimum: 22.2447
#> Joining with `by = join_by(cons_cluster)`
adata_res <- hc_umap(adata_res)
adata_res <- hc_cluster_hulls(adata_res)
hc_plot_umap(adata_res)