plotMap: Visualize expression maps

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

Description

Method visualizes topographical expression maps in two dimensions.

Usage

plotMap(
  sce,
  color_by = c("phenoName", "featureName"),
  name,
  type = c("surface.fit", "surface.se", "raw"),
  samples_only = FALSE
)

Arguments

sce	A SingleCellExperiment object
color_by	Indicates if nodes are colorized by a feature expression
name	A character string specifying the featureName or phenoName
type	Type of map; one of "raw","surface.fit","surface.se"
samples_only	If only individual samples should be colorized rather than the whole surface (default: FALSE)

Details

Two-dimensional visualization of the trajectory. The red line representsthe trajectory and individual points denote samples. This plot type can either show thetopography of a given feature’s expression landscape or colorizes individual samples by a metadata label. The feature is selected by setting the parameter color_type and the respecitve name. To show feature expression, a surface is fitted using isotropic (i.e., same parameters for both map dimensions) thin-plate spline smoothing in gam. It gives an overview of expression dynamics along all branches of the trajectory. The parameter type defines if either the raw/original expression data shoud be shown, the full fitted expression surface should be shown (type="surface.fit") or the standard error of the surface prediction (type="surface.se"), or the expression values of single samples only (type="surface.fit" and only_samples=TRUE).

To show all landmarks on the map, please use the parameters color_by="phenoName" and name="landmark".

Value

A ggplot object

Author(s)

Daniel C. Ellwanger

See Also

gam

Examples

# Example data
data(exSCE)

# Plot landmarks
plotMap(exSCE, color_by="phenoName", name="landmark")

# Plot phenotype
plotMap(exSCE, color_by="phenoName", name="age")

# Plot feature expression map
plotMap(exSCE, color_by="featureName", name="feature_10", type="surface.fit")
plotMap(exSCE, color_by="featureName", name="feature_10", type="surface.fit",
        samples_only=TRUE)

#Plot surface fit standard errors
plotMap(exSCE, color_by="featureName", name="feature_10", type="surface.se")

dcellwanger/CellTrails documentation built on May 12, 2020, 2:01 a.m.