plotPseudotime: Monocle3 Pseudotime

In kueckelj/SPATA: A Toolbox for Spatial Gene Expression Analysis

Monocle3 Pseudotime

Description

A wrapper around monocle3::plot_cells().

Usage

plotPseudotime(
  object,
  use_cds_file = FALSE,
  save_cds_file = FALSE,
  preprocess_method = "PCA",
  cluster_method = "leiden",
  color_to = NULL,
  ...,
  verbose = TRUE
)

Arguments

object	A valid spata-object.
use_cds_file	A directory leading to a .rds file containing a valid cell_data_set-object previously calculated for the specified object. Specified as a character value. If set to FALSE the cell_data_set object will be created from scratch.
save_cds_file	A filename/directory (that does not already exists) under which the used or created cell_data_set-object is going to be stored specified as a character value. Should end with .rds.
preprocess_method	Given to monocle3::preprocess_cds() if use_cds_file isn't a character string.
cluster_method	Given to monocle3::cluster_cells() if use_cds_file isn't a character string.
...	Additional arguments given to monocle3::plot_cells().
verbose	Logical value. If set to TRUE informative messages with respect to the computational progress made will be printed. (Warning messages will always be printed.)

Value

Returns a list of one or two ggplot-objects that can be additionally customized according to the rules of the ggplot2-framework.

• pseudotime: Monocle3-Umap colored by feature 'pseudotime'.

• color_to: Monocle3-Umap colored by input of color_to. (if specified)

kueckelj/SPATA documentation built on March 22, 2022, 9:59 p.m.