add_cyclic_trajectory {dynwrap}R Documentation

Constructs a circular trajectory using the pseudotime values of each cell.

Description

The pseudotime is divided into three equally sized segments, and are placed within a trajectory in the form A -> B -> C -> A

Usage

add_cyclic_trajectory(
  dataset,
  pseudotime,
  directed = FALSE,
  do_scale_minmax = TRUE,
  ...
)

Arguments

dataset

A dataset created by wrap_data() or wrap_expression()

pseudotime

A named vector of pseudo times.

directed

Whether or not the directionality of the pseudotime is predicted.

do_scale_minmax

Whether or not to scale the pseudotime between 0 and 1. Otherwise, will assume the values are already within that range.

...

extra information to be stored in the wrapper.

Value

The dataset object with trajectory information, including:

Examples

library(tibble)
dataset <- wrap_data(cell_ids = letters)

pseudotime <- tibble(cell_id = dataset$cell_ids, pseudotime = runif(length(dataset$cell_ids)))
pseudotime
trajectory <- add_cyclic_trajectory(dataset, pseudotime)

# for plotting the result, install dynplot
#- dynplot::plot_graph(trajectory)

[Package dynwrap version 1.2.2 Index]