monocle3 (version 1.0.0)

choose_graph_segments: Choose cells along the path of a principal graph

Description

Choose cells along the path of a principal graph

Usage

choose_graph_segments(
  cds,
  reduction_method = "UMAP",
  starting_pr_node = NULL,
  ending_pr_nodes = NULL,
  return_list = FALSE,
  clear_cds = TRUE
)

Arguments

cds

CDS object to be subsetted.

reduction_method

The reduction method to plot while choosing cells. Currently only "UMAP" is supported.

starting_pr_node

NULL, or a string with the name of the starting principal node to be used. You can see the principal nodes in your dataset by using plot_cells with label_principal_points = TRUE.

ending_pr_nodes

NULL, or one or more strings with the name(s) of the ending principal node(s) to be used. You can see the principal nodes in your dataset by using plot_cells with label_principal_points = TRUE.

return_list

Logical, return a list of cells instead of a subsetted CDS object.

clear_cds

Logical, clear CDS slots before returning. After clearing the cds, re-run processing from preprocess_cds(), ... Default is TRUE.

Value

A subset CDS object. If return_list = FALSE, a list of cell and graph node names.