plotStateTrajectory: Visualize state trajectory graph

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

Description

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

Usage

1
2
3
4
5
6
7
8
9
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

1
2
3
4
5
6
7
8
9
# 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.