PathwaySpace (version 1.0.1)

silhouetteMapping,PathwaySpace-method: Decorating PathwaySpace images with graph silhouettes.

Description

silhouetteMapping constructs an image baseline used to outline the graph layout in a PathwaySpace image.

Usage

# S4 method for PathwaySpace
silhouetteMapping(pts, baseline = 0.01, pdist = 0.05, verbose = TRUE)

Value

A preprocessed PathwaySpace class object.

Arguments

pts

A PathwaySpace class object.

baseline

A fraction (in [0,1]) of the signal scale of a PathwaySpace image. This term only affects the image baseline projection, which represents a silhouette of the graph's layout outlined in the resulting image. When baseline = 0 (i.e. lower level of the signal scale), the baseline will extend over the entire image space, so no silhouette will be visible.

pdist

A term (in 0,1) determining a distance unit for the signal convolution related to the image space. This distance will affect the extent over which the convolution operation projects the image baseline.

verbose

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

Author

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

See Also

circularProjection

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 graph silhouette
pts <- silhouetteMapping(pts)