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RGraphSpace - A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics

An interface for rendering 'igraph' objects as 'ggplot2' graphics within a normalized coordinate space. 'RGraphSpace' implements new geometries that treat a graph as a single coherent object, synchronizing node and edge layers under standard aesthetic mappings. Node features are resolved on demand, supporting high-dimensional data without expanding node tables. Spatial alignment is available at the pixel level, with node coordinates anchored to pixel centers through a half-pixel offset, enabling precise node positioning over external reference frames such as images and maps.

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7.04 score 5 stars 1 dependents 73 scripts 352 downloads

RedeR - Interactive visualization and manipulation of nested networks

RedeR combines an R package with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.

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guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology

6.96 score 7 dependents 108 scripts 730 downloads

PathwaySpace - Spatial Projection of Network Signals along Geodesic Paths

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 uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices. By combining graph theory, signal processing, and visualization, 'PathwaySpace' provides a way of representing graph data on a continuous projection space. Based on methods introduced in Tercan et al. (2025) <doi:10.1016/j.xpro.2025.103681> and Ellrott et al. (2025) <doi:10.1016/j.ccell.2024.12.002>.

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bioinformaticsbiological-networksgraph

5.83 score 2 stars 26 scripts 302 downloads

TreeAndLeaf - Displaying binary trees with focus on dendrogram leaves

TreeAndLeaf implements a hybrid layout strategy that enhances leaf-level visualization in dendrograms. By integrating force-directed graph and tree layout algorithms, it enables projection of multiple layers of information onto graph–tree diagrams.

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graphandnetworknetworkvisualizationdatarepresentationsoftwaresystemsbiologybinary-treebinary-tree-visualizationdendrogramreorganizing-dendrograms

5.45 score 15 stars 31 scripts 428 downloads