store_multiple_seurat_reductions.r

library(Seurat)
library(harmony)

# x is a Seurat object not yet processed but we have chosen num_pc
x <- FindNeighbors(x, reduction = 'pca', dims = 1:num_pc, verbose = FALSE) %>%
  FindClusters(verbose = FALSE, resolution = 0.2) %>%
  RunUMAP(reduction = 'pca', dims = 1:num_pc, verbose = FALSE)
x$noharmony_clusters <- x$seurat_clusters
x@misc$noharmony_umap <- x@reductions$umap

x <- RunHarmony(x, 'strain', theta = 1, dims.use = 1:num_pc, max.iter.harmony = 100) %>%
	FindNeighbors(reduction = 'harmony', dims = 1:num_pc) %>%
	FindClusters(verbose = FALSE, resolution = 0.2) %>%
	RunUMAP(dims = 1:num_pc, reduction = 'harmony')
x$harmony_clusters <- x$seurat_clusters
x@misc$harmony_umap <- x@reductions$umap