trajLayout-set: SET trajectory layout

In CellTrails: Reconstruction, visualization and analysis of branching trajectories

Description

Sets layout used for trajectory visualization to a SingleCellExperiment object.

Usage

trajLayout(object, adjust) <- value

Arguments

object	An object of class SingleCellExperiment
adjust	Indicates if layout has to be adjusted such that edge lengths correlate to pseudotime (default: TRUE)
value	A data.frame with x- and y-coordinates for each sample (rows = samples, columns = coordinates)

Details

CellTrails implements a module which can incorporate pseudotime information into the the graph layout (activated via parameter adjust). Here, edge lengths between two nodes (samples) will then correspond to the inferred pseudotime that separates two samples along the trajectory.

Diagnostic messages

An error is thrown if the number of rows of the layout does not correspond to the number of trajectory samples or if the number of columns is less than 2, or if the row names do not correspond to sampleNames.

Value

An updated object of class SingleCellExperiment

Author(s)

Daniel C. Ellwanger

See Also

write.ygraphml trajSampleNames

Examples

# Example data
data(exSCE)
tl <- trajLayout(exSCE)

trajLayout(exSCE) <- tl

CellTrails documentation built on Nov. 8, 2020, 5:53 p.m.