network-drawing

Script with different solutions to draw monolayer and multilayer networks in R.

Ecological Synthesis Lab (SintECO).

Authors: Marco Mello & Renata Muylaert.

E-mail: marmello@usp.br.

First published on April 25th, 2017 (English version).

Run in R version 4.0.2 (2020-06-22) -- "Taking Off Again".

Disclaimer: You may use this software freely for any purposes at your own risk. We assume no responsibility or liability for the use of this software, convey no license or title under any patent, copyright, or mask work right to the product. We reserve the right to make changes in the software without notification. We also make no representation or warranty that such application will be suitable for the specified use without further testing or modification. If this software helps you produce any academic work (paper, book, chapter, dissertation, report, talk, lecture or similar), please acknowledge the authors and cite the source, using this repo's DOI or URL.

List of folders and files

1. data (folder)

   a. net1.txt -> interactions of pollination between oil-collecting bees and oil flowers (Bezerra et al. 2009).

   b. net2.txt -> interactions of pollination between bats, hawkmoths, and plants (Queioz et al. 2020).

   c. net3an.txt -> interactions of seed destruction (antagonism) between marsupials, rodents, and plants (Genrich et al. 2017).

   d. net3mu.txt -> interactions of seed dispersal (mutualism) between marsupials, rodents, and plants (Genrich et al. 2017).

2. figures (folder)

   a. net1_bipartite_graph.png -> monolayer network drawn as a bipartite graph, vertex colors by class.

   b. net1_bipartite_matrix_modules.png -> monolayer network drawn as an incidence matrix with the modules identified.

   c. net1_bipartite_matrix.png -> monolayer network drawn as an incidence matrix.

   d. net1_igraph_graph_modules_bi.png -> monolayer network drawn as an energy-minimization graph, vertex colors by module. Modularity analyzed in the package bipartite.

   e. net1_igraph_graph_modules_ig.png -> monolayer network drawn as an energy-minimization graph, vertex colors by module. Modularity analyzed in the package igraph.

   f. net1_igraph_graph_multi.png -> multilayer network drawn as an energy-minimization graph, with multiple taxonomic groups, each identified by a different color.

   g. net1_igraph_graph_taxon.png -> monolayer network drawn as an energy-minimization graph, with multiple taxonomic groups, each identified by a different color.

   h. net1_igraph_graph.png -> monolayer network drawn as an energy-minimization graph, vertex colors by class.

   i. net2_igraph_graph_modules_ig.png -> monolayer network drawn as an energy-minimization graph, with multiple taxonomic groups, vertex colors by module, vertex shapes by taxon. Modularity analyzed in the package igraph.

3. MyTriangle.R -> additional function to create the diamond shape used to represent some vertex types. This is a modification of the "mytriangle" function provided in the igraph manual.

4. network-drawing.R -> script with commented codes.

Data sources

1. net1 -> Bezerra, E. L. S., Machado, I. C., & Mello, M. A. R. (2009). Pollination networks of oil-flowers: a tiny world within the smallest of all worlds. Journal of Animal Ecology, 78(5), 1096–1101.

2. net2 -> Queiroz, J. A., Diniz, U. M., Vázquez, D. P., Quirino, Z. M., Santos, F. A. R., Mello, M. A. R., & Machado, I. C. (2020). Bats and hawkmoths form mixed modules with flowering plants in a nocturnal interaction network. Biotropica, accepted. See also this repo.

3. net3an and net3mu -> Genrich, C. M., Mello, M. A. R., Silveira, F. A. O., Bronstein, J. L., & Paglia, A. P. (2017). Duality of interaction outcomes in a plant-frugivore multilayer network. Oikos, 126(3), 361–368. doi: 10.1111/oik.03825

Instructions

Follow the instructions provided in the script "network-drawing.R".

Feedback

If you have any questions, corrections, or suggestions, please feel free to open and issue or make a pull request.

Acknowledgments

We thank our labmates and our sponsors, especially the Alexander von Humboldt-Stiftung, CNPq, CAPES, and FAPESP, who gave us grants, fellowships, and scholarships. Pedro Jordano and Carsten Dormann helped us take our first steps in analyzing and drawing networks in R. Special thanks go to Katherine Ognyanova, who gave us invaluable tips on advanced network drawing in R. We strongly recommend her online tutorial. Last, but not least, we thank the Stack Overflow Community, where we solve most of our coding dilemmas. A dilemma related to converting incidence matrices to make a multilayer network was solved here.

Suggested readings

If you want to understand the theory behind this script, read the following works:

• Barabasi, A.L. (2016) Network Science, 1st ed. Cambridge University Press, Cambridge.

• Bascompte, J. & Jordano, P. (2014) Mutualistic Networks, 1st ed. Princeton University Press, Princeton.

• Beckett, S. J. (2016). Improved community detection in weighted bipartite networks. Royal Society Open Science, 3(1), 140536. doi: 10.1098/rsos.140536

• Blondel, V. D., Guillaume, J.-L., Lambiotte, R., & Lefebvre, E. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment, 2008(10), P10008.

• Marai, G. E., B. Pinaud, K. Bühler, A. Lex, and J. H. Morris. (2019) Ten simple rules to create biological network figures for communication. PLOS Comput. Biol. 15: e1007244.

• Mello MAR, Muylaert RL, Pinheiro RBP & Félix GMF. 2016. Guia para análise de redes ecológicas. Edição dos autores, Belo Horizonte. 112 p. ISBN-13: 978-85-921757-0-2.

• Ognyanova K. 2019. Static and dynamic network visualization with R.

• Pocock, M. J. O., D. M. Evans, C. Fontaine, M. Harvey, R. Julliard, Ó. McLaughlin, J. Silvertown, A. Tamaddoni-Nezhad, P. C. L. White, and D. A. Bohan. (2016) The Visualisation of Ecological Networks, and Their Use as a Tool for Engagement, Advocacy and Management. In G. Woodward and D. A. Bohan (Eds.) Advances in Ecological Research. pp. 41–85, Academic Press, Cambridge.