order_cells: Orders cells according to pseudotime.

In cole-trapnell-lab/monocle3: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

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.

Usage

order_cells(
  cds,
  reduction_method = "UMAP",
  root_pr_nodes = NULL,
  root_cells = NULL,
  verbose = FALSE
)

Arguments

cds	the cell_data_set upon which to perform this operation
reduction_method	a string specifying the reduced dimension method to use when ordering cells. Currently only "UMAP" is supported.
root_pr_nodes	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.
root_cells	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.
verbose	Whether to show running information for order_cells

Value

an updated cell_data_set object.

cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.