ggvis vs. ggplot2+Shiny; which one to choose for interactive visualization?
Well, many months have been passed from this help request. I write this answer to my own request in order to share my experience. I learned ggplot2 and then ggvis as well as Shiny. Shiny can work with both of them, but I found ggvis more structured and lucid comparing to ggplot2. Something which is expectable as the former is being developed based on the development experience of the latter. Moreover, ggvis seems much faster than ggplot2 in quick graph/chart generation, it seems much more suitable for 'Shiny' and creating an applet. However, the negative point is the lack of many features in ggvis since the package is under development and has not become matured yet. 

And many thanks to comments here. I have checked Gephi, it wouldn't help. I created my applet which works really fine, however I finally reached to this point that I need to use more powerful tools such as d3js, as one has already suggested.