trajLayout<- {CellTrails} | R Documentation

## SET trajectory layout

### 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

[Package CellTrails version 1.4.0 Index]