Dear Sir or Madam:
I followed the tutorial for q2-SCNIC and exported the network qza using qiime tools export. When I imported the network.gml file into Cytoscape, no network showed up. When I open the nework.gml, it looks:
graph [
node [
id 0
label “109c4e6920d3cc765c1f298b7668f43b”
module “m;o;d;u;l;e;;2;0"
]
node [
id 1
label “9839136c88371e1863e1547c441251a3”
]
node [
id 2
label “206774702744b609a8a557362708f6aa”
]
node [
id 3
label “d5e73c259f22065dc7b1427e7b8554e4”
module "m;o;d;u;l;e;;6;4”
]
node [
id 4
label “2699c0529711356e6650389930efe1cf”
module “m;o;d;u;l;e;;2;2"
]
node [
id 5
label “6630f2e2bd0c6976bcf769a425c5149b”
module "m;o;d;u;l;e;;2;9”
]
node [
id 6
label “6ddfafb041d410a5dbdf040501d2a989”
module “m;o;d;u;l;e;;1;4;4"
]
node [
id 7
label “977909f104c0b057bc461fb47a60c6cf”
module "m;o;d;u;l;e;;5”
]
node [
id 8
label “16876cb6a8143937e7733982d35bb56b”
module “m;o;d;u;l;e;;5;4"
]
node [
id 9
label “474a4007a020e95a306518cb6da6399b”
module "m;o;d;u;l;e;;1;3;1”
]
node [
id 10
label “af62a419dfda19a54212d570e1819bf1”
module “m;o;d;u;l;e;;2;5"
]
node [
id 11
label “a6b8618cffdb60d49baf8f805aaa5ccd”
module "m;o;d;u;l;e;;1;3;3”
]
node [
id 12
label “73d328f43bed7964d6c18f71757e3536”
module “m;o;d;u;l;e;;5;3"
]
node [
id 13
label “93250b09e4e3b9b135d078d7728957fc”
module "m;o;d;u;l;e;;7;4”
]
node [
id 14
label “fa58951b6eef437400122ceb2c6c7ad3”
module “m;o;d;u;l;e;;1;0"
]
node [
id 15
label “8819135be42cbdf08e8e15b1bd2b8c7b”
module "m;o;d;u;l;e;;1;4;6”
]
node [
id 16
label “385df82967d549f79708cb76735f5d5e”
module “m;o;d;u;l;e;;1;1;8"
]
node [
id 17
label “65089434b33bb68fa9053a4aa99a7097”
]
node [
id 18
label “301df8f3a851e0ef34a0f7346f2d2bae”
module "m;o;d;u;l;e;;4;1”
]
node [
id 19
label “5015f98de99d891a5c149315f2950f0a”
module “m;o;d;u;l;e;;1;4;2"
]
node [
id 20
label “3f261e90a4baffca17837bff51bc536e”
module "m;o;d;u;l;e;;1;6;4”
]
I am wondering what is wrong with my data or anything else.
How are you loading it into cytoscape? I use import network from file on my files generated with q2-SCNIC. Is this the entire file or just a part of it? This seems to only be the node portion of the gml and not the entire graph with edges.
And also sorry for all the extra semicolons. I have fixed that bug and it will be pushed in the next update to q2-SCNIC.
I suspect without the full file, the edges won’t make any sense since they reference other nodes at the beginning of the file. Maybe you could upload it to a service like dropbox so that @michael.shaffer has the full information?
Hey sorry about not responding to this. Thesis writing is taking over my life.
@1621447326
This looks like a valid network file to me. So when you open the network.gml file with Cytoscape you don’t get an error but just a blank canvas where the network should be? What do you see? I know with some versions of Cytoscape you can’t really see the network until you tell it to space out the nodes. Have you tried hitting the Apply Preferred Layout button after loading the network into Cytoscape? That might make it so that you can see what the network looks like.
Have you tried hitting that button that looks like a refresh button on the toolbar in that screenshot? If you click that does the graph spread out? This function is also called Apply Preferred Layout.
I would highly recommend filtering your data in some way before using SCNIC. Low abundance OTUs will affect the ability of sparCC to calculate reliable correlations and increase run time.
