Dimensional reduction

Code

# Enrique Blanco Carmona
# e.blancocarmona@kitz-heidelberg.de
# PhD Student – Clinical Bioinformatics
# Division of Pediatric Neurooncology (B062)
# DKFZ-KiTZ | Germany

#--------------------------------------------------------------------
# 5 - DIMENSIONAL REDUCTION
#--------------------------------------------------------------------

sample <- Seurat::RunPCA(sample, assay = "SCT")
elbow <- Seurat::ElbowPlot(sample) # Visualize the number of PCs and select an appropriate number.
npcs <- 15 # Selected number of PCs.

# Normalize using Harmony. The effect to remove is the orig.ident metadata column (from where each sample comes from).
sample <- harmony::RunHarmony(sample, dims = 1:npcs, group.by.vars = "orig.ident", assay.use = "SCT")

# Dimensional reduction: UMAP over harmony reduction.
sample <- Seurat::RunUMAP(sample, dims = 1:npcs, reduction = "harmony")

sample <- Seurat::FindNeighbors(sample, dims = 1:npcs, reduction = "harmony")

sample <- Seurat::FindClusters(sample,
                               random.seed = 42)