Question: visualization of chromatin interaction networks
0
gravatar for Bogdan
10 months ago by
Bogdan550
Palo Alto, CA, USA
Bogdan550 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 • 188 views
ADD COMMENTlink modified 10 months ago by Aaron Lun23k • written 10 months ago by Bogdan550
Answer: visualization of chromatin interaction networks
0
gravatar for Aaron Lun
10 months ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k 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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Aaron Lun23k

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

ggraph : https://www.data-imaginist.com/2017/ggraph-introduction-layouts/

ggnet2: https://briatte.github.io/ggnet/

networkD3 : http://christophergandrud.github.io/networkD3/

visnetwork : http://datastorm-open.github.io/visNetwork/edges.html

ADD REPLYlink modified 10 months ago • written 10 months ago by Bogdan550
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