Inferring a trajectory inference using Monocle DDRTree

Source: R/ti_monocle_ddrtree.R

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 = "DDRTree", max_components = 2L,
  norm_method = "vstExprs", auto_param_selection = TRUE,
  run_environment = NULL)

Arguments

reduction_method

discrete; A character string specifying the algorithm to use for dimensionality reduction. (default: "DDRTree"; values: "DDRTree")
max_components

integer; The dimensionality of the reduced space (default: 2L; range: from 2L to 20L)
norm_method

discrete; Determines how to transform expression values prior to reducing dimensionality (default: "vstExprs"; values: "vstExprs", "log", "none")
auto_param_selection

logical; 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.
run_environment

In which environment to run the method, can be "docker" or "singularity".

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.