Question: visualization of chromatin interaction networks
0
13 months ago by
Bogdan570
Palo Alto, CA, USA
Bogdan570 wrote:

Dear all,

please would you advise if there is any tool in BioC that could help with  the visualization of CHROMATIN INTERACTION NETWORKS as a GRAPH (where NODES="chromosome loci", and EDGES = "interactions").  Thanks a lot !

-- bogdan

ggbio gviz karyotyper • 233 views
modified 13 months ago by Aaron Lun24k • written 13 months ago by Bogdan570
Answer: visualization of chromatin interaction networks
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13 months ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

While this isn't my forte, I thought I'd respond here to your offline message, just in case anyone else cares:

library(InteractionSet)
example(GInteractions)
anc <- anchors(gi, type="both", id=TRUE)

library(igraph)
G <- make_graph(rbind(anc$first, anc$second),
n=length(regions(gi)), directed=FALSE)
plot(G)

... or see ?layouts for the available graph layouts.

Thanks a lot, Aaron, for your reply : it is always great to hear from you. Yes, I've embraced so far the same strategy, i.e. to use the package "igraph" (http://kateto.net/network-visualization), although I am also looking into :

tidygraph : https://github.com/thomasp85/tidygraph