addTrail: ADD trail

In elldc/CellTrails: Reconstruction, visualization and analysis of branching trajectories

Description

Function to define a single trail on the trajectory.

Usage

addTrail(sce, from, to, name)

Arguments

sce	An object of class SingleCellExperiment
from	Start landmark
to	End landmark
name	Name of trail

Details

A trajectory can be composed of multiple single trails (e.g., developmental progression from a common start towards distinct terminal phenotypes). Start and endpoints of trails can be identified visually using the plot function plotMap. Here, start (=from) and end (=to) IDs of landmarks are starting with the character "B" (for branching points), "H" (for trail heads, i.e. terminal nodes), and "U" for user-defined landmarks.

Diagnostic messages

An error is thrown if the trajectory has not been fitted yet. Please, call fitTrajectory first. Further, an error is thrown if the provided start or end ID is unknown. A warning is shown if a trail with the same name already exists and gets re-defined.

Value

An updated object of class SingleCellExperiment

Author(s)

Daniel C. Ellwanger

See Also

fitTrajectory landmarks plotMap

Examples

# Example data
data(exSCE)

# Add trail
exSCE <- addTrail(exSCE, "H1", "H2", "Tr3")
trailNames(exSCE)
phenoNames(exSCE)

elldc/CellTrails documentation built on May 16, 2020, 4:40 a.m.