plotMap {CellTrails} | R Documentation |
Method visualizes topographical expression maps in two dimensions.
plotMap(sce, color_by = c("phenoName", "featureName"), name, type = c("surface.fit", "surface.se", "raw"), samples_only = FALSE)
sce |
A |
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) |
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"
.
A ggplot
object
Daniel C. Ellwanger
gam
# 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")