Supervised Annotation

# RDS object and annotation genesets are loaded.


Seurat::DefaultAssay(sample) <- "RNA"
# This computes Enrichment scores and sets them up as an assay.
out <- SCpubr::do_EnrichmentHeatmap(sample, input_gene_list = nmf_markers, flavor = "UCell", return_object = TRUE)

# Retrieve the Seurat object.
sample <- out$Object

# Scale data and perform dimensional reduction.
sample <- Seurat::ScaleData(sample)
sample <- Seurat::RunPCA(sample, features = rownames(sample))
sample <- Seurat::RunUMAP(sample, dims = 1:7)
sample <- Seurat::FindNeighbors(sample, reduction = "pca", dims = 1:7)
sample <- Seurat::FindClusters(sample, reduction = "pca", dims = 1:7)

# Annotate clusters with clear enrichment.