Distance to trajectory

[jblich870]

Hi,

Is it possible to extract a value for each cell of shortest distance to a given trajectory? In the Trajectory Analysis part of the tutorial it states that "ArchR aligns all cells to the trajectory based on their Euclidean distance to the nearest point along the manifold". I wondered whether this distance was stored or able to be retrieved. I would like to use this to compute cell weights for each trajectory in my dataset (similar to output by Slingshot) to input into Tradeseq.

Many thanks,
J

[rcorces]

This isnt currently stored anywhere but it wouldnt be hard to implement. Will try to do so this week. In the meantime, you could modify the addTrajectory() function to store the object dfTrajectory3 somewhere. Thats where you will find the distance.

ArchR/R/Trajectory.R

Lines 238 to 251 in b7a2e8f

	dfTrajectory3$Trajectory <- 100 * .getQuantiles(dfTrajectory3[,2])
	#Add To ArchR Project
	ArchRProj <- addCellColData(
	ArchRProj = ArchRProj,
	data = dfTrajectory3$Trajectory,
	name = name,
	cells = rownames(dfTrajectory3),
	force = force
	)
	.endLogging(logFile = logFile)
	ArchRProj

[rcorces]

ArchR/R/Trajectory.R

Lines 26 to 27 in c8b9071

	#' @param saveDF A full or relative path to use for creating a `.RDS` R object file containing a DataFrame with additional information about the trajectory.
	#' This includes the distance of each cell to the splines of the trajectory and the corresponding indicies returned by `nabor::knn`.

[jblich870]

Ah yes, thanks. This is perfect, thank you for attending to this so quickly!

[rcorces]

is that confirmation that it works on your end?

[jblich870]

Yes, works well this end. Thank you!

[rcorces]

Merged to dev via #1673