find_curve: Find curve

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Find curve

Description

Find pseudo-time curve using the princurve library, given the gene path. Alternative to the findPaths method.

Usage

find_curve(
  object,
  metadata,
  column,
  population_sequence,
  dims.use,
  reduction.type
)

Arguments

object	CellRouter object.
metadata	data frame; metadata table with cell annotations.
column	character; column in the metadata table specifying whether transitions are between clusters or other annotations, such as sorted populations.
population_sequence	list of character vectors; the ordered sequence of the populations that will be used to calculate the curve.
dims.use	numeric vector; the number of dimensions to use.
reduction.type	character; the dimension reduction space to be used: pca, tsne, DC of diffusion components, umap, or custom.

Value

data frame; the cells, their distance from the origin of the curve, and the curve they belong.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.