trajLayout<- {CellTrails} | R Documentation |
Sets layout used for trajectory visualization to a
SingleCellExperiment
object.
trajLayout(object, adjust) <- value
object |
An object of class |
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) |
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
.
An updated object of class SingleCellExperiment
Daniel C. Ellwanger
write.ygraphml
trajSampleNames
# Example data data(exSCE) tl <- trajLayout(exSCE) trajLayout(exSCE) <- tl