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Mapping Summits on PathwaySpace Images

Source: R/pspaceMethods.R
summitMapping-methods.Rd

The summitMapping method implements a segmentation strategy to identify summits on a 2D-landscape image (see summitWatershed).

Usage

# S4 method for class '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 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.

See also

circularProjection

Author

Sysbiolab Team

Examples

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

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