Description Usage Arguments Details Value Author(s) See Also Examples
Method visualizes topographical expression maps in two dimensions.
1 2 3 4 5 6 7 |
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<e2><80><99>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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # 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")
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