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PathwaySpace (version 1.0.2)

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

188

Version

1.0.2

License

Artistic-2.0

Issues

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Maintainer

Mauro Castro

Last Published

July 28th, 2025

Functions in PathwaySpace (1.0.2)

pspace.cols

A simple vector of colors for PathwaySpace images
polarProjection,PathwaySpace-method

Spatial Projection of Graph-Associated Signals
signalAggregation

Signal aggregation functions
signalDecay

Signal decay functions
plotPathwaySpace,PathwaySpace-method

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

Decorating PathwaySpace Images with Graph Silhouettes
summitMapping,PathwaySpace-method

Mapping Summits on PathwaySpace Images
weibullDecay

Weibull decay function
vertexSignal,PathwaySpace-method

Accessor Functions for PathwaySpace Objects
summitWatershed

Variation of the watershed algorithm for summit detection
buildPathwaySpace

Constructor of PathwaySpace-class Objects
expDecay

Exponential decay function
PCv12_pruned_igraph

A pruned and laid out igraph object from Pathway Commons V12
gs_vertex_attr<-,PathwaySpace-method

Accessor Functions for PathwaySpace Objects
getPathwaySpace,PathwaySpace-method

Accessors for Fetching Slots from a PathwaySpace Object
PathwaySpace-class

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

Spatial Projection of Graph-Associated Signals
linearDecay

A simple linear decay function
gimage

An image matrix
CGC_20211118

COSMIC-CGC genes mapped to PathwaySpace images
Hallmarks_v2023_1_Hs_symbols

A list with Hallmark gene sets (v2023.1)
PathwaySpace-package

PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths
pathDistances

Calculate a pathway space distance between two vectors
plotPathDistances

Accessory function to plot pathway space distances