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I'm trying to create a network visualization to study the flights to and from a certain airport.

My data consists of 123000 rows in this format:

Origin_ID    Destination_ID    Frequency
  1726            3504           40000
  3504            4517              40
  5616            7205              38
               ...

I'm trying to create a image similar to this:

enter image description here

Basically, I want to be able to see the strength of the relationship (based on the frequency) and identify which combinations are most common in that airport.

Can it be created in R using this format? Or do you suggest any other open source platform to create this visualization?

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The visNetwork R package is the best I've worked with. It renders with the vis.js Javascript package right in your RStudio window. Nodes and edge visualization is fully customizable and may be data-driven. They implement click-functionality on your graphs, so you can rearrange them or highlight a node and its neighbors. I've found people really enjoy this in presentations, and the highlight functionality is great for making static PowerPoint presentations or figures.

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