Question: visualization of chromatin interaction networks
0
gravatar for Bogdan
8 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 • 158 views
ADD COMMENTlink modified 8 months ago by Aaron Lun23k • written 8 months ago by Bogdan550
Answer: visualization of chromatin interaction networks
0
gravatar for Aaron Lun
8 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 8 months ago • written 8 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 8 months ago • written 8 months ago by Bogdan550
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 154 users visited in the last hour