fitTrajectory: Align samples to trajectory

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

Description

Orthogonal projection of each sample to the trajectory backbone.

Usage

fitTrajectory(sce)

Arguments

sce	A SingleCellExperiment object

Details

The previously selected component (with k states) defines the trajectory backbone. With this function CellTrails embeds the trajectory structure in the latent space by computing k-1 straight lines passing through k mediancentres (Bedall & Zimmermann, 1979) of adjacent states. Then, a fitting function is learned. Each sample is projected to its most proximal straight line passing through the mediancentre of its assigned state. Here, whenever possible, projections on line segments between two mediancentres are preferred. Residuals (fitting deviations) are given by the Euclidean distance between the sample's location and the straight line. Finally, a weighted acyclic trajectory graph can be constructed based on each sample’s position along its straight line. In addition, data vectors are connected to mediancentres to enable the proper determination of branching points. Each edge is weighted by the distance between each node (sample) after orthogonal projection.

Of note, the fitting function implies potential side branches in the trajectory graph; those could be caused due to technical variance or encompass samples that were statistically indistinguishable from the main trajectory given the selected genes used for trajectory reconstruction.

Diagnostic messages

An error is thrown if an trajectory graph component was not computed or selected yet; functions connectStates and selectTrajectory need to be run first.

Value

An updated SingleCellExperiment object

Author(s)

Daniel C. Ellwanger

References

Bedall, F.K., and Zimmermann, H. (1979). Algorithm AS143. The mediancentre. Appl Statist 28, 325-328.

See Also

connectStates selectTrajectory

Examples

# Example data
data(exSCE)

# Align samples to trajectory
exSCE <- fitTrajectory(exSCE)

dcellwanger/CellTrails documentation built on May 12, 2020, 2:01 a.m.