write.ygraphml: Export trajectory graph
In CellTrails: Reconstruction, visualization and analysis of branching trajectories

Description Usage Arguments Details Value Author(s) See Also Examples

Writes graphml file containing the trajectory graph's structure.

write.ygraphml(
  sce,
  file,
  color_by = c("phenoName", "featureName"),
  name,
  node_label = "state"
)

`sce`	A `SingleCellExperiment` object
`file`	Character string naming a file
`color_by`	Indicates if nodes are colorized by a feature expression ('featureName') or phenotype label ('phenoName')
`name`	A character string specifying the featureName or phenoName
`node_label`	Defines the node label name (optional). Can be either set to the samples' states ('state') or the samples' names ('name').

To visualize the trajectory graph, a proper graph layout has to be computed. Ideally, edges should not cross and nodes should not overlap (i.e., a planar embedding of the graph). CellTrails enables the export and import of the trajectory graph structure using the graphml file format. This file format can be interpreted by most third-party graph analysis applications, allowing the user to subject the trajectory graph to a wide range of (tree) layout algorithms. In particular, its format has additional ygraph attributes best suited to be used with the Graph Visualization Software 'yEd' which is freely available from yWorks GmbH (http://www.yworks.com/products/yed) for all major platforms.

The colors of the nodes can be defined by the parameters color_by and name. Please note that the trajectory landmarks are indicated by setting color_by='phenoName' and name='landmark'. States can be indicated by color_by='phenoName' and name='state'.

If a layout is already present in the provided CellTrailsSet object, the samples' coordinates will be listed in the graphml file.

Diagnostic messages

An error is thrown if the trajectory has not been computed yet; function fitTrajectory needs to be called first. Feature names and phenotype names get checked and will throw an error if not contained in the dataset. Please note, the parameter name is case-sensitive.

write.ygraphml returns an invisible NULL

Daniel C. Ellwanger

fitTrajectory featureNames phenoNames

# Example data
data(exSCE)

## Not run: 
# Export trajectory graph structure to graphml
# Color nodes by gene expression (e.g, feature_10)
write.ygraphml(sce, file="yourFilePath", color_by="featureName",
              name="feature_10")

# Color nodes by metadata (e.g., state) and
# label nodes by the (simulated) age of each sample
write.ygraphml(sce, file="yourFilePath", color_by="phenoName",
              name="state", node_label="age")

# Color and label nodes by landmark type and id
write.ygraphml(sce, file="yourFilePath", color_by="phenoName",
              name="landmark", node_label="landmark")
## End(Not run)