add_linear_trajectory {dynwrap}

R Documentation

Constructs a linear trajectory using pseudotime values

Description

Constructs a linear trajectory using pseudotime values

Usage

add_linear_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 the trajectory will be directed.
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 trajectory

Value

The dataset object with trajectory information, including:

• milestone_ids: The names of the milestones, a character vector.

• milestone_network: The network between the milestones, a dataframe with the from milestone, to milestone, length of the edge, and whether it is directed.

• divergence_regions: The regions between three or more milestones where cells are diverging, a dataframe with the divergence id (divergence_id), the milestone id (milestone_id) and whether this milestone is the start of the divergence (is_start)

• milestone_percentages: For each cell its closeness to a particular milestone, a dataframe with the cell id (cell_id), the milestone id (milestone_id), and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the milestone).

• progressions: For each cell its progression along a particular edge of the milestone_network. Contains the same information as milestone_percentages. A dataframe with cell id (cell_id), from milestone, to milestone, and its percentage (a number between 0 and 1 where higher values indicate that a cell is close to the to milestone and far from the from milestone).

Examples

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

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

trajectory <- add_linear_trajectory(dataset, pseudotime)

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