Chapter 2 Overview

The following illustrates the typical sequence of steps performed during a CellTrails analysis and lists the available functions, respectively.

  • Selection of trajectory features
    • filterTrajFeaturesByDL
    • filterTrajFeaturesByCOV
    • filterTrajFeaturesByFF
  • Lower-dimensional manifold learning
    • embedSamples
    • findSpectrum
    • latentSpace
    • plotManifold
  • Clustering
    • findStates
    • states
    • plotStateSize
    • plotStateExpression
  • Determination of the trajectory topology
    • connectStates
    • showTrajInfo
    • trajComponents
    • selectTrajectory
    • plotStateTrajectory
  • Chronologically ordering of samples
    • fitTrajectory
    • plotTrajectoryFit
  • Trajectory visualization
    • write.ygraphml
    • read.ygraphml
    • trajLayout
    • plotMap
  • Identification of paths (trails) on the trajectory
    • landmarks
    • userLandmarks
    • addTrail, removeTrail
    • trailNames
    • trails
    • plotTrail
  • Inference of expression dynamics of trails
    • fitDynamic
    • plotDynamic
  • Intra- and inter-trail expression dynamic comparison
    • contrastTrailExpr

By calling the function showTrajInfo, an informative overview of the data relevant for, or stored by CellTrails is printed. We suggest to use this function multiple times during a CellTrails analysis, as it provides useful insights into the analysis’ progress.

showTrajInfo(exBundle)
## [[ CellTrails ]] 
## logcounts: 183 features, 1008 samples
## Pheno data: 
##   sampleNames: "Cell-1-1" "Cell-1-2" ... "Cell-11-82" (1008)
##   phenoNames: "fm143" "origin" (2)
## Feature data: 
##   featureNames: "ABCA5" "ARF1" ... "USH2A" (183)
##   rowData: none
## Trajectory data: 
##   trajFeatureNames: "ABCA5" "ARF1" ... "USH2A" (183)
##   latentSpace: none
##   states: none
## Trajectories: none
##   trajSampleNames: "Cell-1-1" "Cell-1-2" ... "Cell-11-82" (1008)
##   trajResiduals: MSE=NA
##   landmarks: none
##   trajLayout: none
## Trail data: 
##   trailNames: none

The entries logcounts and Feature data correspond to the expression matrix and feature information provided and annotated by the user, respectively. Pheno data contains metainformation for each sample stored by the user and by CellTrails. The entries Trajectory data, Trajectories and Trail data denote CellTrails specific information and will be described in detail in the respective section of this handbook.