I am attempting to create a bipartite network graph for virus-bat host matrix data rather than virus-macaque data (see the quote from the article below):
Source: "Non-random patterns in viral diversity" by Simon J. Anthony, et. al., Nature Communications, 22 Sep 2015."A presence/absence matrix was constructed to show the distribution of viruses across all samples, and used for network and statistical analyses as described in the main text. In summary, A bipartite (two-mode) affiliation network was generated for virus–macaque host matrix data, stratified by site name, and a unipartite (one-mode) virus:virus net- work was generated to display the connections between viruses. Network analyses and visualisation were conducted in the network analysis platform Gephi, using the force-directed algorithm ForceAtlas2 (ref. 28)."
I have two spreadsheets:
- one with bat species as the row names and the columns with the site names with values for the number of bat species present at each site
one with virus species as the row names and the columns with the site names with values for the number of virus species present at each site.
Here are my questions:
1) a) What is a node?
b) What is an edge?
c) How are they related in Gephi?
d) Where can I find tutorials or postings that explain this information?
2) a) With the format for the spreadsheets described above, can I create a bipartite network graph?
b) If not, then how should I format my spreadsheets?
c) Is there any specific format needed for the spreadsheet files to be imported into Gephi for bipartite or monopartite network analysis?
3) Where can I find tutorials with step-by-step instructions on creating bipartite or monopartite network graphs from creating the spreadsheet files to completion of the figures?
I'm sorry that I have so many questions. I haven't found the User Guides nor Gephi Tutorials helpful with answering my questions and showing step-by-step directions from start to finish.
Thank you in advance.