I've noticed that in some cases (when I used the igraph package to create a network from a data frame and then transform it to graphNEL object), the layout is not consistent for specified properties. I'm not sure if this is a real issue, but I think it is worth checking.
I used the fruchterman-rheingold layout (the layout number 10), set a layout using the gravity_multiplier property and plotted the network (case 1), then set a layout using the attraction_multiplier property and plotted the network (case 2) -the layout changed (as expected). Next, I set a layout using the gravity_multiplier property again (case 1'). When I plotted the network for the case 1', the layout looked very similar to the one for case 2, and quite different from the one in case 1 (and I was expecting the opposite).
When I used the cyPlot function to create a network, I did not have this issue.
I've noticed that in some cases (when I used the igraph package to create a network from a data frame and then transform it to graphNEL object), the layout is not consistent for specified properties. I'm not sure if this is a real issue, but I think it is worth checking.
I used the fruchterman-rheingold layout (the layout number 10), set a layout using the gravity_multiplier property and plotted the network (case 1), then set a layout using the attraction_multiplier property and plotted the network (case 2) -the layout changed (as expected). Next, I set a layout using the gravity_multiplier property again (case 1'). When I plotted the network for the case 1', the layout looked very similar to the one for case 2, and quite different from the one in case 1 (and I was expecting the opposite).
When I used the cyPlot function to create a network, I did not have this issue.
Code and session info are available at https://gist.github.com/Vessy/6c9567f26f397320ae849445ac92a981 (RCy3_example1.R is the example with igraph and RCy3_example2.R is the example with cyPlot).
I did not check if the same happens for different layouts or properties.
Thanks!