PCv12_pruned_igraph

gdist.toy

<p>This igraph object was created from a 'sif' file available from 
the Pathway Commons V12 (Rodchenkov et al., 2020), which was filtered to 
keep interactions from the following sources: CTD, Recon, HumanCyc, 
DrugBank, MSigDB, DIP, BioGRID, IntAct, BIND, and PhosphoSite. The igraph 
was additionally pruned and laid out by a force-directed algorithm aiming 
signal projection on PathwaySpace's images. Edges with the smallest 
betweenness centrality were pruned using 'backward elimination' and
'forward selection' strategies. The resulting graph represents the 
main connected component with the minimum number of edges.</p>

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.

Mauro Castro

PathwaySpace

Spatial Projection of Network Signals along Geodesic Paths

Vinicius Chagas

Victor Apolonio

PCv12_pruned_igraph function

Format

<p>Chris Wong, Mauro Castro, and TCGA Network.</p>

Author

A pruned and laid out igraph object from Pathway Commons V12. — PCv12_pruned_igraph

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

PCv12_pruned_igraph: A pruned and laid out igraph object from Pathway Commons V12.

Description

Usage

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Author

References

Examples