Package: ExplodeLayout 0.1.2
ExplodeLayout: Calculate Exploded Coordinates Based on Original Node Coordinates and Node Clustering Membership
Current layout algorithms such as Kamada Kawai do not take into consideration disjoint clusters in a network, often resulting in a high overlap among the clusters, resulting in a visual “hairball” that often is uninterpretable. The ExplodeLayout algorithm takes as input (1) an edge list of a unipartite or bipartite network, (2) node layout coordinates (x, y) generated by a layout algorithm such as Kamada Kawai, (3) node cluster membership generated from a clustering algorithm such as modularity maximization, and (4) a radius to enable the node clusters to be “exploded” to reduce their overlap. The algorithm uses these inputs to generate new layout coordinates of the nodes which “explodes” the clusters apart, such that the edge lengths within the clusters are preserved, while the edge lengths between clusters are recalculated. The modified network layout with nodes and edges are displayed in two dimensions. The user can experiment with different explode radii to generate a layout which has sufficient separation of clusters, while reducing the overall layout size of the network. This package is a basic version of an earlier version called [epl]<https://github.com/UTMB-DIVA-Lab/epl> that searched for an optimal explode radius, and offered multiple ways to separate clusters in a network (Bhavnani et al(2017) <PMID: 28815099>). The example dataset is for a bipartite network, but the algorithm can work also for unipartite networks.
Authors:
ExplodeLayout_0.1.2.tar.gz
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ExplodeLayout_0.1.2.tgz(r-4.4-any)ExplodeLayout_0.1.2.tgz(r-4.3-any)
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ExplodeLayout.pdf |ExplodeLayout.html✨
ExplodeLayout/json (API)
NEWS
# Install 'ExplodeLayout' in R: |
install.packages('ExplodeLayout', repos = c('https://weibzhan.r-universe.dev', 'https://cloud.r-project.org')) |
- example_incidmat - Sample dataset of a bipartite network..
- example_nodelist - Example nodelist file of a bipartite network.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:f423523df5. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-win | OK | Oct 31 2024 |
R-4.5-linux | OK | Oct 31 2024 |
R-4.4-win | OK | Oct 31 2024 |
R-4.4-mac | OK | Oct 31 2024 |
R-4.3-win | OK | Oct 31 2024 |
R-4.3-mac | OK | Oct 31 2024 |
Exports:explode_coordinatesget_edgelist_from_incidmatget_explode_nodelistget_nodelist_for_plottingplot_binet_ggplot2
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Sample dataset of a bipartite network.. | example_incidmat |
Example nodelist file of a bipartite network. | example_nodelist |
Explode the old coordinates using cluster membership | explode_coordinates |
Generate edgelist from incidence matrix of a bipartite network | get_edgelist_from_incidmat |
Explode the old coordinates using cluster membership and generate nodelist for plotting | get_explode_nodelist |
Format a nodelist for plotting using the new coordinates found by ExplodeLayout | get_nodelist_for_plotting |
Plot bipartite network given node list (label, coordinates, shape, color) and incidence matrix. | plot_binet_ggplot2 |