C-overview.Rmd

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# Overview
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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.

```{r, eval=TRUE}
showTrajInfo(exBundle)
```

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.