choose_graph_segments: Choose cells along the path of a principal graph

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

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.

cole-trapnell-lab/monocle3 documentation built on June 11, 2025, 11:22 p.m.