plotMap {CellTrails} | R Documentation

## Visualize expression maps

### 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")

[Package CellTrails version 1.10.0 Index]