Seurat to Phate to Seurat

Seurat and Phate

### handles the Seurat to phate conversio

### first, grab the input required for phate (here we are using the normalized data stored in Seurat
seurat_data <- as.data.frame(seurat.object@assays$RNA@data)

## reshape for input into PHATE
phate_data_input <- t(seurat_data)

## run phate -- this is a default run, feel free to tune params
phate_output <- phate(phate_data_input) 

## quick sanity check of the phate embeddings
ggplot(phate_output, aes(x=PHATE1, y=PHATE2)) +
  geom_point()

## stash the embeddings back into the seurat object as a dimension reduction object
seurat.object[["PHATE"]] <- CreateDimReducObject(embeddings = phate_output$embedding, key = "PHATE_", assay = DefaultAssay(seurat.object))

## plot using seurat's default tools
DimPlot(seurat.object , reduction = "PHATE") + ggtitle(label = "PHATE")