PhenoPath

Will generate a trajectory using PhenoPath.

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

ti_phenopath(thin = 40L, z_init = "1", model_mu = FALSE,
  scale_y = TRUE)

Arguments

thin

The number of iterations to wait each time before re-calculating the elbo. Domain: U(2, 500). Default: 40. Format: integer.
z_init

The initialisation of the latent trajectory. Should be one of* A positive integer describing which principal component of the data should be used for initialisation (default 1), or * The text character "random", for random initialisation from a standard normal distribution. Domain: 1, 2, 3, 4, 5, random. Default: 1. Format: character.
model_mu

Logical - should a gene-specific intercept term be modelled?. Default: FALSE. Format: logical.
scale_y

Logical - should the expression matrix be centre scaled?. Default: TRUE. Format: logical.

Value

A TI method wrapper to be used together with infer_trajectory

References

Campbell, K., Yau, C., 2017. Uncovering genomic trajectories with heterogeneous genetic and environmental backgrounds across single-cells and populations.