Correlate Trajectories

This function will correlate 2 trajectory matrices from getTrajectory.

correlateTrajectories(
  seTrajectory1 = NULL,
  seTrajectory2 = NULL,
  corCutOff = 0.5,
  varCutOff1 = 0.8,
  varCutOff2 = 0.8,
  removeFromName1 = c("underscore", "dash"),
  removeFromName2 = c("underscore", "dash"),
  useRanges = FALSE,
  fix1 = "center",
  fix2 = "start",
  maxDist = 250000,
  log2Norm1 = TRUE,
  log2Norm2 = TRUE,
  force = FALSE,
  logFile = createLogFile("correlateTrajectories")
)

Arguments

seTrajectory1

A SummarizedExperiment object that results from calling getTrajectory().

seTrajectory2

A SummarizedExperiment object that results from calling getTrajectory().

corCutOff

A numeric describing the cutoff for determining correlated features.

varCutOff1

The "Variance Quantile Cutoff" to be used for identifying the top variable features across seTrajectory1. Only features with a variance above the provided quantile will be retained.

varCutOff2

The "Variance Quantile Cutoff" to be used for identifying the top variable features across seTrajectory2. Only features with a variance above the provided quantile will be retained.

removeFromName1

A character vector describing how to filter names in matrix 1. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept.

removeFromName2

A character vector describing how to filter names in matrix 2. Options include "underscore", "dash", "numeric" and "dot". The string portion prior to these will be kept.

useRanges

A boolean describing whether to use range overlap matching for correlation analysis.

fix1

A character describing where to resize the coordinates of seTrajectory1. Options include "start", "center", "end".

fix2

A character describing where to resize the coordinates of seTrajectory2. Options include "start", "center", "end".

maxDist

A integer specifying the maximum distance between the coordinates of seTrajectory1 and seTrajectory2 for computing correlations.

log2Norm1

A boolean describing whether to log2 normalize seTrajectory1.

log2Norm2

A boolean describing whether to log2 normalize seTrajectory2.

force

A boolean value that determines whether analysis should continue if resizing coordinates in seTrajectory1 or seTrajectory2 does not align with the strandedness. Only when useRanges = TRUE.

logFile

The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

#Add Trajectory
proj <- addTrajectory(proj, trajectory = c("C1", "C2", "C3"), embedding = "UMAP", force = TRUE)

#Get Trajectories
seTraj1 <- getTrajectory(proj, useMatrix = "GeneScoreMatrix")
seTraj2 <- getTrajectory(proj, useMatrix = "GeneIntegrationMatrix")

#Correlate
corTraj <- correlateTrajectories(seTraj1, seTraj2, corCutOff = 0.35, varCutOff1 = 0.6, varCutOff2 = 0.6)