Inferring a trajectory inference using topslam

Source: R/ti_topslam.R

Will generate a trajectory using topslam.

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

ti_topslam(n_components = 2L, n_neighbors = 10L, linear_dims = 0L,
  max_iters = 1000L, dimreds = c(TRUE, TRUE, TRUE, TRUE, TRUE),
  run_environment = NULL)

Arguments

n_components

integer; The number of components (default: 2L; range: from 2L to 10L)
n_neighbors

integer; The number of neighbors (default: 10L; range: from 2L to 100L)
linear_dims

integer; (default: 0L; range: from 0L to 5L)
max_iters

integer; The number of iterations to optimize over (default: 1000L; range: from 10L to 10000L)
dimreds

logical_vector; Which dimensionality reductions to use; tSNE, PCA, Spectral, Isomap and/or ICA
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

Zwiessele, M., Lawrence, N.D., 2016. Topslam: Waddington Landscape Recovery for Single Cell Experiments.