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.