summitMapping,PathwaySpace-method {PathwaySpace} | R Documentation |
Mapping summits on PathwaySpace images.
Description
The summitMapping
method implements a segmentation
strategy to identify summits on a 2D-landscape image
(see summitWatershed
).
Usage
## S4 method for signature 'PathwaySpace'
summitMapping(
pts,
maxset = 30,
minsize = 30,
threshold = 0.5,
verbose = TRUE,
segm_fun = summitWatershed,
...
)
Arguments
pts |
A PathwaySpace class object. |
maxset |
A single positive integer indicating the maximum number of summits to be returned by the segmentation function. |
minsize |
A single positive integer indicating the minimum size of the summits. |
threshold |
A threshold provided as a fraction (in |
verbose |
A single logical value specifying to display detailed
messages (when |
segm_fun |
A segmentation function used to detect summits
(see |
... |
Additional arguments passed to the segmentation 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)
# Map summits in a 2D-landscape image
pts <- summitMapping(pts)