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)



A character string specifying the algorithm to use for dimensionality reduction. Domain: ICA. Default: ICA. Format: character.


The dimensionality of the reduced space. Domain: U(2, 20). Default: 2. Format: integer.


Determines how to transform expression values prior to reducing dimensionality. Domain: vstExprs, log, none. Default: log. Format: character.


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.


Whether to include monocle feature filtering. Default: TRUE. Format: logical.


Minimal mean feature expression, only used when filter_features is set to TRUE. Domain: U(0, 10). Default: 0.1. Format: numeric.


A TI method wrapper to be used together with infer_trajectory


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.