plotStateTrajectory: Visualize state trajectory graph
In CellTrails: Reconstruction, visualization and analysis of branching trajectories

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

Method visualizes the state-to-state relations delineating the trajectory backbone.

plotStateTrajectory(
  sce,
  color_by = c("phenoName", "featureName"),
  name,
  component = NULL,
  point_size = 3,
  label_offset = 2,
  recalculate = FALSE
)

`sce`	A `SingleCellExperiment` object
`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
`component`	Component of trajectory graph that should be shown (integer value)
`point_size`	Adjusts the point size of the data points shown
`label_offset`	Adjusts the offset of the data point labels
`recalculate`	If layout should be re-drawn (default: FALSE)

Shows a single tree component of the computed trajectory graph. Each point in this plot represents a state and can be colorized according to feature expression (mean expression per state) or experimental metadata (arithmetic mean or percentage distribution of categorial values). The component is defined by parameter component. If the trajectory graph contains only a single component, then this parameter can be left undefined. The points' coloration can be defined via the attributes color_by and name, respectively. Missing sample lables are recovered using nearest neighbor learning.
If the state trajectory graph layout was set with stateTrajLayout<- then the layout will be reused for visualization.

A ggplot object

Daniel C. Ellwanger

connectStates

# Example data
data(exSCE)

plotStateTrajectory(exSCE, color_by="phenoName", name="age",
                    component=1, point_size = 1.5, label_offset = 4)

gp <- plotStateTrajectory(exSCE, color_by="featureName", name="feature_1",
                          component=1, recalculate=TRUE)
stateTrajLayout(exSCE) <- gp