summitMapping-methods: Mapping Summits on PathwaySpace Images

In PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths

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(
  ps,
  maxset = 30,
  minsize = 30,
  threshold = 0.5,
  verbose = TRUE,
  segm_fun = summitWatershed,
  ...
)

Arguments

ps	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.

Value

A preprocessed PathwaySpace class object.

Author(s)

Mauro Castro and TCGA Network.

See Also

circularProjection

Examples

# Load a large igraph
data("PCv12_pruned_igraph", package = "PathwaySpace")

# Continue this example from the PathwaySpace vignette,
# in the 'PathwaySpace decoration' section

PathwaySpace documentation built on Aug. 8, 2025, 6:47 p.m.