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PathwaySpace (version 1.1.1)

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 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 graph data.

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Install

install.packages('PathwaySpace')

Monthly Downloads

194

Version

1.1.1

License

Artistic-2.0

Issues

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Maintainer

Mauro Castro

Last Published

February 28th, 2026

Functions in PathwaySpace (1.1.1)

summitMapping,PathwaySpace-method

Mapping Summits on PathwaySpace Images
signalDecay

Deprecated function
silhouetteMapping,PathwaySpace-method

Decorating PathwaySpace Images with Graph Silhouettes
summitWatershed

Variation of the watershed algorithm for summit detection
polarDecay

Polar transformation functions
weibullDecay

Constructor of Weibull decay functions
vertexSignal,PathwaySpace-method

Accessor Functions for PathwaySpace Objects
getPathwaySpace,PathwaySpace-method

Accessors for Fetching Slots from a PathwaySpace Object
CGC_20211118

COSMIC-CGC genes mapped to PathwaySpace images
expDecay

Constructor of exponential decay functions
circularProjection,PathwaySpace-method

Circular Projection of Graph-Associated Signals
buildPathwaySpace

Constructor of PathwaySpace-class Objects
PathwaySpace-class

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

Accessor Functions for PathwaySpace Objects
signalAggregation

Signal aggregation functions
pspace.pals

Create interpolated color palettes for PathwaySpace images
plotPathDistances

Accessory function to plot pathway space distances
pathDistances

Calculate a pathway space distance between two vectors
linearDecay

Constructor of linear decay functions
polarProjection,PathwaySpace-method

Polar Projection of Graph-Associated Signals
pspace.cols

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

Plotting 2D-landscape images for the PathwaySpace package
PathwaySpace-package

PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths
gimage

An image matrix
PCv12_pruned_igraph

A pruned and laid out igraph object from Pathway Commons V12
Hallmarks_v2023_1_Hs_symbols

A list with Hallmark gene sets (v2023.1)