Hi, for my RNA-Seq data from two species, I did the consensus analysis using WGCNA to identify conserved modules between the two species. My question is regarding the visualization of these modules:
As expected, for conserved modules (say module-1), only the connections for a few hub genes are well conserved between the two species. Relaxing the module networks in VisANT yields very different looking networks for the two species. This makes it difficult to visually compare the two species networks with ease.
Is there a way to freeze the layout of the network from speciesX and only change the TO values to that of speciesY, such that the differences in connections are obvious but the layout of two networks remains the same?
One way to do it, would be to manually change the position of the hubs-of-interest in a circle-layout, but this layout is not impressive visually in showing 'hubness' of the genes. Hoping to get some pointers on how to go about it. Thanks!