ti_merlot: MERLoT

In dynverse/dynmethods: A collection of trajectory inference methods

MERLoT

Description

Will generate a trajectory using MERLoT.

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

Usage

ti_merlot(
  sigma = "local",
  distance = "euclidean",
  ndim = 20L,
  density_norm = TRUE,
  n_local = c(5L, 7L),
  w_width = 0.01,
  n_components_to_use = 3L,
  N_yk = 100L,
  lambda_0 = 8e-10,
  mu_0 = 0.0025,
  increaseFactor_mu = 20L,
  increaseFactor_lambda = 20L,
  FixEndpoints = FALSE
)

Arguments

sigma	Diffusion scale parameter of the Gaussian kernel. A larger sigma might be necessary if the eigenvalues can not be found because of a singularity in the matrix. Must a character vector – "local" (default) or "global". Domain: local, global. Default: local. Format: character.
distance	A character vector specifying which distance metric to use. Allowed measures are the Euclidean distance (default), the cosine distance (1-corr(c_1, c_2)), or the rank correlation distance (1-corr(rank(c_1), rank(c_2))). Domain: euclidean, cosine, rankcor. Default: euclidean. Format: character.
ndim	Number of eigenvectors/dimensions to return. Domain: U(2, 20). Default: 20. Format: integer.
density_norm	Logical. If TRUE, use density normalisation. Default: TRUE. Format: logical.
n_local	If sigma == 'local', the n_local nearest neighbor(s) determine(s) the local sigma. Domain: ( U(2, 20), U(2, 20) ). Default: (5, 7). Format: integer_range.
w_width	Window width to use for deciding the branch cutoff. Domain: e^U(-9.21, 0.00). Default: 0.01. Format: numeric.
n_components_to_use	Which components to use in downstream analysis. Domain: U(2, 20). Default: 3. Format: integer.
N_yk	Number of nodes for the elastic principal tree. Domain: U(2, 1000). Default: 100. Format: integer.
lambda_0	Principal elastic tree energy function parameter. Domain: e^U(-27.63, -13.82). Default: 8e-10. Format: numeric.
mu_0	Principal elastic tree energy function parameter. Domain: U(5e-04, 0.005). Default: 0.0025. Format: numeric.
increaseFactor_mu	Factor by which the mu will be increased for the embedding. Domain: U(2, 50). Default: 20. Format: numeric.
increaseFactor_lambda	Factor by which the mu will be increased for the embedding. Domain: U(2, 50). Default: 20. Format: numeric.
FixEndpoints	Documentation not provided by authors. Default: FALSE. Format: logical.

Value

A TI method wrapper to be used together with infer_trajectory

References

Parra, R.G., Papadopoulos, N., Ahumada-Arranz, L., Kholtei, J.E., Mottelson, N., Horokhovsky, Y., Treutlein, B., Soeding, J., 2018. Reconstructing complex lineage trees from scRNA-seq data using MERLoT.

dynverse/dynmethods documentation built on Jan. 18, 2024, 4:44 a.m.