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

6.88 score 7 dependents 121 scripts 719 downloads

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

An interface to integrate 'igraph' and 'ggplot2' graphics within a normalized coordinate system. 'RGraphSpace' implements geometric objects based on 'ggplot2' prototypes, optimized for the representation of large networks. The package provides three specialized 'geoms' to translate graph data into geometric layers, supporting customization of aesthetics and visual styles. These 'geoms' use a dual-anchor normalization approach to align layers, required for analyses where network elements must be referenced to a spatial map. 'RGraphSpace' aims to facilitate side-by-side visualization of multiple graphs spatially aligned with reference maps and images.

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6.36 score 2 stars 1 dependents 45 scripts 538 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

5.42 score 15 stars 29 scripts 407 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

5.38 score 2 stars 7 scripts 499 downloads