Dataset Information

Crosslink: An R Package for Network Visualization of Grouped Nodes.

ABSTRACT: The demand for network visualization of relationships between nodes attributed to different categories grows in various biomedical research scenarios, such as gene regulatory networks, drug-target networks, ligand-receptor interactions and association networks of multi-omics elements. Elegantly visualizing the relationships between nodes with complex metadata of nodes and edges appended may inspire new insights. Here, we developed the crosslink R package, tailored for network visualization of grouped nodes, to provide a series of flexible functions for generating network diagrams. We first designed a CrossLink class for storage of metadata about nodes and edges and manipulation of node coordinates. Then affine transformation and function mapping transformation are implemented to perform fundamental node coordinates transformation by groups, based on which various network layouts can be defined easily. For convenience, we predefined several commonly used layouts, including row, column, arc, polygon and hive, which also can be combined in one layout. Finally, we designed a user-friendly wrapper function to draw network connections, aesthetic mappings of metadata and decoration with related annotation graphs in one interface by taking advantage of the powerful ggplot2 system. Overall, the crosslink R package is easy-to-use for achieving complex visualization of a network diagram of grouped nodes surrounded by associated annotation graphs.

Availability and implementation

Cosslink is an open-source R package, freely available from github: https://github.com/zzwch/crosslink; A detailed user documentation can be found in https://zzwch.github.io/crosslink/.

SUBMITTER: Liu D

PROVIDER: S-EPMC8322777 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundNetwork analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exist for generating and analyzing such networks, either from correlation scores or the absolute value of a transformed score called weighted topological overlap (wTO). However, since gene regulatory processes can up- or down-regulate genes, it is of great interest to explicitly consider both positive and negative correlations when constructing a gene co-expression network.ResultsHere, we present an R package for calculating the weighted topological overlap (wTO), that, in contrast to existing packages, explicitly addresses the sign of the wTO values, and is thus especially valuable for the analysis of gene regulatory networks. The package includes the calculation of p-values (raw and adjusted) for each pairwise gene score. Our package also allows the calculation of networks from time series (without replicates). Since networks from independent datasets (biological repeats or related studies) are not the same due to technical and biological noise in the data, we additionally, incorporated a novel method for calculating a consensus network (CN) from two or more networks into our R package. To graphically inspect the resulting networks, the R package contains a visualization tool, which allows for the direct network manipulation and access of node and link information. When testing the package on a standard laptop computer, we can conduct all calculations for systems of more than 20,000 genes in under two hours. We compare our new wTO package to state of art packages and demonstrate the application of the wTO and CN functions using 3 independently derived datasets from healthy human pre-frontal cortex samples. To showcase an example for the time series application we utilized a metagenomics data set.ConclusionIn this work, we developed a software package that allows the computation of wTO networks, CNs and a visualization tool in the R statistical environment. It is publicly available on CRAN repositories under the GPL -2 Open Source License ( https://cran.r-project.org/web/packages/wTO/ ).

Dataset Information

Crosslink: An R Package for Network Visualization of Grouped Nodes.

Availability and implementation

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets