Assigns cells a pseudotime value based on their projection on the principal
graph learned in the learn_graph function and the position of chosen
root states. This function takes as input a cell_data_set and returns it
with pseudotime information stored internally.
order_cells() optionally takes "root" state(s) in the form of cell
or principal graph node IDs, which you can use to specify the start of the
trajectory. If you don't provide a root state, an plot will be generated
where you can choose the root state(s) interactively. The trajectory will be
composed of segments.
order_cells(
cds,
reduction_method = "UMAP",
root_pr_nodes = NULL,
root_cells = NULL,
verbose = FALSE
)the cell_data_set upon which to perform this operation
a string specifying the reduced dimension method to use when ordering cells. Currently only "UMAP" is supported.
NULL or a vector of starting principal points. If
provided, pseudotime will start (i.e. be zero) at these graph nodes. You
can find the principal point names by running plot_cells with
label_principal_points = TRUE. Both root_pr_nodes and
root_cells cannot be provided.
NULL or a vector of starting cells. If provided,
pseudotime will start (i.e. be zero) at these cells. Both
root_pr_nodes and root_cells cannot be provided.
Whether to show running information for order_cells
an updated cell_data_set object.