I am trying to handle Hi-C data to represent interactions between DNA segments. I got the data from the ENCODE publication of Shen et al 2012, Nature, in which, for each chromosome, interactions are represented as a file containing the matrix of interaction. Considering that each bin represent 40kb in the chromosome, I could isolate rows and columns covering my sequence of interest and I used heatmap.2 to generate the 'half' heatmap of interactions. In parallele, I used the same coordinates to generate a Gviz track showing the genes present in the region as well as ChIP-Seq peaks. And finally, I am interested in merging the two figures together to visually determine which genes/epigenetic marks are in interacting domains. For the moment, I tried to do it manually but even if the size of both graphics should be the same, I can not precisely align the two figures. So, I am wondering if there could be a way to do it automatically?
Thank you very much.