Monocle DDRTree

Will generate a trajectory using Monocle DDRTree.

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

ti_monocle_ddrtree(reduction_method = "ICA", 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: ICA. Default: ICA. 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.