Choose cells along the path of a principal graph. Modified from Monocle3 function choose_graph_segments to allow for selection of multiple branches and zooming in.
choose_path.RdChoose cells along the path of a principal graph. Modified from Monocle3 function choose_graph_segments to allow for selection of multiple branches and zooming in.
Usage
choose_path(
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.