PathwaySpace (version 1.0.2)

buildPathwaySpace: Constructor of PathwaySpace-class Objects

Description

buildPathwaySpace is a constructor of PathwaySpace-class objects.

Usage

buildPathwaySpace(
  gs,
  nrc = 500,
  verbose = TRUE,
  g = deprecated(),
  mar = deprecated()
)

Value

A pre-processed PathwaySpace class object.

Arguments

gs

A GraphSpace object. Alternatively, an igraph object with node coordinates assigned to x and y vertex attributes, and node labels assigned to name vertex attribute.

nrc

A single positive integer indicating the number of rows and columns (in pixels) for a square image matrix. This argument will affect the resulting image size and resolution.

verbose

A single logical value specifying to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE).

g

Deprecated from PathwaySpace 1.0.1; use 'gs' instead.

mar

Deprecated from PathwaySpace 1.0.1; use 'mar' in GraphSpace instead.

Author

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

See Also

undirected_graph

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# Check graph validity
gs <- GraphSpace(gtoy1, mar = 0.1)

# Create a new PathwaySpace object
ps <- buildPathwaySpace(gs, nrc = 100)
# note: adjust 'nrc' to increase image resolution