circularProjection,PathwaySpace-method {PathwaySpace} | R Documentation |
Creating 2D-landscape images from graph objects.
Description
circularProjection
implements a convolution
algorithm to project signal across a 2D-coordinate system.
Usage
## S4 method for signature 'PathwaySpace'
circularProjection(
pts,
kns = 8,
pdist = 0.15,
rescale = TRUE,
verbose = TRUE,
decay_fun = weibullDecay,
knn = deprecated(),
...
)
Arguments
pts |
A PathwaySpace class object. |
kns |
A single positive integer determining the k-nearest signal sources used in the signal convolution operation. |
pdist |
A term (in |
rescale |
A single logical value indicating whether to rescale
the signal. If the signal |
verbose |
A single logical value specifying to display detailed
messages (when |
decay_fun |
A signal decay function. Available: 'Weibull',
'exponential', and 'linear' functions (see |
knn |
Deprecated from PathwaySpace 1.0; use 'kns' instead. |
... |
Additional arguments passed to the decay function. |
Value
A preprocessed PathwaySpace class object.
Author(s)
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
See Also
Examples
# Load a demo igraph
data('gtoy1', package = 'PathwaySpace')
# Create a new PathwaySpace object
pts <- buildPathwaySpace(gtoy1, nrc = 100)
# note: adjust 'nrc' to increase image resolution
# Create a 2D-landscape image
pts <- circularProjection(pts)