Skip to contents

Computation of Diffusion Map and Diffusion Pseudo Time

diff_map.Rd

The functions computes a Diffusion Map and Diffusion Pseudo Time using package destiny.

Usage

diff_map(scMuffinList = NULL, root_cell = "random", n_pcs = 50, ...)

Arguments

scMuffinList

scMuffinList object

root_cell

root cell or "random" to pick up a random root via the destiny::random_root function

n_pcs

number of PCs to consider, 50 by default

...

parameters passed to destiny::DiffusionMap

Value

scMuffinList with element "diffusion_map_pseudo_t", a list with summary and full. summary is a data.frame with: the first two eigenvectors; branch, branch label for each cell; tips, whether the cell is a tip of the branching. full contains dpt object, generated by [destiny::DPT()]. See destiny for further information.