plotStateTrajectory: Visualize state trajectory graph

In elldc/CellTrails: Reconstruction, visualization and analysis of branching trajectories

Description

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

Usage

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

Arguments

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)

Details

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.

Value

A ggplot object

Author(s)

Daniel C. Ellwanger

See Also

connectStates

Examples

# 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

elldc/CellTrails documentation built on May 16, 2020, 4:40 a.m.