ti_monocle_ddrtree: Monocle DDRTree

In dynverse/dynmethods: A collection of trajectory inference methods

Monocle DDRTree

Description

Will generate a trajectory using Monocle DDRTree.

This method was wrapped inside a container. The original code of this method is available here.

Usage

ti_monocle_ddrtree(
  reduction_method = "DDRTree",
  max_components = 2L,
  norm_method = "log",
  auto_param_selection = TRUE,
  filter_features = TRUE,
  filter_features_mean_expression = 0.1
)

Arguments

reduction_method	A character string specifying the algorithm to use for dimensionality reduction. Domain: DDRTree. Default: DDRTree. Format: character.
max_components	The dimensionality of the reduced space. Domain: U(2, 20). Default: 2. Format: integer.
norm_method	Determines how to transform expression values prior to reducing dimensionality. Domain: vstExprs, log, none. Default: log. Format: character.
auto_param_selection	When this argument is set to TRUE (default), it will automatically calculate the proper value for the ncenter (number of centroids) parameters which will be passed into DDRTree call. Default: TRUE. Format: logical.
filter_features	Whether to include monocle feature filtering. Default: TRUE. Format: logical.
filter_features_mean_expression	Minimal mean feature expression, only used when filter_features is set to TRUE. Domain: U(0, 10). Default: 0.1. Format: numeric.

Value

A TI method wrapper to be used together with infer_trajectory

References

Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H.A., Trapnell, C., 2017. Reversed graph embedding resolves complex single-cell trajectories. Nature Methods 14, 979–982.

dynverse/dynmethods documentation built on Jan. 18, 2024, 4:44 a.m.