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PathwaySpace (version 1.0.1)

Spatial Projection of Network Signals along Geodesic Paths

Description

For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data.

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Install

install.packages('PathwaySpace')

Monthly Downloads

267

Version

1.0.1

License

Artistic-2.0

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Maintainer

Mauro Castro

Last Published

April 8th, 2025

Functions in PathwaySpace (1.0.1)

polarProjection,PathwaySpace-method

Creating 2D-landscape images from graph objects.
buildPathwaySpace

Constructor of PathwaySpace-class objects.
pspace.cols

A simple vector of colors for PathwaySpace images.
silhouetteMapping,PathwaySpace-method

Decorating PathwaySpace images with graph silhouettes.
plotPathwaySpace,PathwaySpace-method

Plotting 2D-landscape images for the PathwaySpace package.
names,PathwaySpace-method

Accessor functions for PathwaySpace objects.
weibullDecay

Weibull decay function.
linearDecay

A simple linear decay function.
vertexWeight,PathwaySpace-method

Accessor functions for fetching slots from a PathwaySpace object.
vertexSignal,PathwaySpace-method

Accessor functions for fetching slots from a PathwaySpace object.
gtoys

Toy 'igraph' objects.
summitWatershed

Variation of the watershed algorithm for summit detection.
length,PathwaySpace-method

Accessor function for PathwaySpace objects.
summitMapping,PathwaySpace-method

Mapping summits on PathwaySpace images.
PathwaySpace-package

PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths
PathwaySpace-class

PathwaySpace: An S4 class for signal propagation on image spaces.
circularProjection,PathwaySpace-method

Creating 2D-landscape images from graph objects.
getPathwaySpace,PathwaySpace-method

Accessors for fetching slots from a PathwaySpace object.
expDecay

Exponential decay function.
pathDistances

Calculate a pathway space distance between two vectors.
Hallmarks_v2023_1_Hs_symbols

A list with Hallmark gene sets (v2023.1).
PCv12_pruned_igraph

A pruned and laid out igraph object from Pathway Commons V12.
gimage

An image matrix.
CGC_20211118

COSMIC-CGC genes mapped to PathwaySpace images.
plotPathDistances

Accessory function to plot pathway space distances.