summitMapping,PathwaySpace-method: 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 PathwaySpace
summitMapping(
  pts,
  maxset = 30,
  minsize = 30,
  threshold = 0.5,
  verbose = TRUE,
  segm_fun = summitWatershed,
  ...
)

Value

A preprocessed PathwaySpace class object.

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 [0,1]) of the max signal intensity.
verbose: A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).
segm_fun: A segmentation function used to detect summits (see summitWatershed).
...: Additional arguments passed to the segmentation function.

Author

Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.

Examples

Run this code

# 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)