Two-mode affiliation network for virus bat host network

[iembry16]

Hi, I previously made a post (http://gephi.forumatic.com/viewtopic.php?f=4&t=5638) asking for assistance in getting started with Gephi to make some network graphs concerning viruses and their bat hosts.

I have tried to make a figure similar to Figure 3 in the (http://www.nature.com/articles/ncomms9147) in the Nature Communications article in Gephi version 0.9.1, but I have been unsuccessful.

I can shade the viruses gray, but I'm having trouble with 1) the size of nodes indicating abundance and 2) colored nodes for the individual bat species colored by the different sites.

Is this possible to implement in Gephi 0.9.1?

The previous post shows the layout of the nodes and the edges.

Thank you.

Irucka

[eduramiba]

You should be able to achieve that by using the Appearance window.
You want to 'partition' the nodes color by site column, and apply 'ranking' of nodes size by the abundance column.

Just make sure your columns don't have empty/null values and this bug: https://github.com/gephi/gephi/issues/1459

[eduramiba]

Some good resources to learn Gephi:

http://www.clementlevallois.net/gephi/t ... ets_en.pdf
https://gephi.org/users/
http://www.clementlevallois.net/gephi.html

[iembry16]

I have attached a screenshot for Gephi 0.9.1.

.

Prior to posting the aforementioned question earlier this weekend, I went through the Filters on the right hand side and came across Partition. I selected Type (Node) and clicked on the Queries, but I couldn't find anything in there to assist me with my question.

Also, I clicked on the "Switch to Ranking" icon/button and it does not do anything. I don't know if it's a bug or if it has not been implemented yet.

The colored boxes next to virus, bat, and site only allow me to change the color for the type and not based on a value.

Most, if not all, of the tutorials, user guides, etc. deal with Gephi versions prior to 0.9.1 which has been frustrating for a new Gephi user as there isn't always a direct equivalent between what you're being shown and Gephi 0.9.1.

For the layout shown in the attachment, can you tell me how to "'partition' the nodes color by site column, and apply 'ranking' of nodes size by the abundance column.""?

I had tried to search for this answer for Gephi 0.9.1 and I had tried to figure it out on my own through going through all of the icons prior to posting the question and again today, but to no avail.

Thank you.

Irucka

[eduramiba]

I think you are encountering this bug: https://github.com/gephi/gephi/issues/1459
We will soon release updates for 0.9.1

[iembry16]

Thank you for your prompt responses.

I have recently used version 0.8.2 beta in addition to 0.9.1. Will the features that were available in the previous version re-appear in 0.9.1 in addition to fixing the bugs?

Thank you.

Irucka

[eduramiba]

Some plugins are already available and others should eventually be too, they just need to be migrated