ti_paga: PAGA

In dynverse/dynmethods: A collection of trajectory inference methods

PAGA

Description

Will generate a trajectory using PAGA.

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

Usage

ti_paga(
  filter_features = TRUE,
  n_neighbors = 15L,
  n_comps = 50L,
  n_dcs = 15L,
  resolution = 1L,
  embedding_type = "fa",
  connectivity_cutoff = 0.05
)

Arguments

filter_features	Whether to do feature filtering. Default: TRUE. Format: logical.
n_neighbors	Number of neighbours for knn. Domain: U(1, 100). Default: 15. Format: integer.
n_comps	Number of principal components. Domain: U(0, 100). Default: 50. Format: integer.
n_dcs	Number of diffusion components for denoising graph, 0 means no denoising. Domain: U(0, 40). Default: 15. Format: integer.
resolution	Resolution of louvain clustering, which determines the granularity of the clustering. Higher values will result in more clusters. Domain: U(0.1, 10). Default: 1. Format: numeric.
embedding_type	Either 'umap' (scales very well, recommended for very large datasets) or 'fa' (ForceAtlas2, often a bit more intuitive for small datasets). Domain: umap, fa. Default: fa. Format: character.
connectivity_cutoff	Cutoff for the connectivity matrix. Domain: U(0, 1). Default: 0.05. Format: numeric.

Value

A TI method wrapper to be used together with infer_trajectory

References

Wolf, F.A., Hamey, F.K., Plass, M., Solana, J., Dahlin, J.S., Göttgens, B., Rajewsky, N., Simon, L., Theis, F.J., 2019. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology 20.

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