I returned a Seurat object with a diffusion map by
seurat_object <- RunDiffusion(seurat_object,genes.use = email@example.com)
Now, how I could know the order of a cell's projection onto this principal curve representing its predicted progression through the development by fitting a principal curve on my diffusion map?
I know Seurat slot for DM1 and DM2 is inside the seurat@dr
fit=principal_curve(as.matrix(seurat_object@firstname.lastname@example.org)) plot(fit) line(fit) points(fit)
I draw this graph of my cells
But how I know the first and last cells on curve? I mean how I know cells from each cluster is being placed where on the curve? By
fit$ord I will obtain orders of cells on the line but how I know the first and end of the line?????