q2-SCNIC output network did not show up when imported into cytoscape


(Yang) #1

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.

Regards,


(Nicholas Bokulich) #2

Thanks for reporting @1621447326! I am passing this on to the developer of this plugin, @michael.shaffer


(Michael Shaffer) #3

Hey @1621447326,

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.

Mike


(Yang) #4

Hi, Mike,
I used “import – network – file” to load the data.
That is just the first part of the data. I failed to upload the gml file or paste the entire content of it.
Here is the last part of the gml file:
source 508
target 547
r 0.47420000000000001
]
edge [
source 509
target 522
r 0.38529999999999998
]
edge [
source 509
target 545
r 0.39799999999999996
]
edge [
source 509
target 518
r 0.53820000000000001
]
edge [
source 509
target 533
r 0.41010000000000002
]
edge [
source 509
target 554
r 0.50119999999999998
]
edge [
source 509
target 558
r 0.4365
]
edge [
source 509
target 510
r 0.39350000000000002
]
edge [
source 509
target 563
r 0.3664
]
edge [
source 510
target 540
r 0.36480000000000001
]
edge [
source 510
target 522
r 0.37030000000000002
]
edge [
source 510
target 563
r 0.38009999999999999
]
edge [
source 510
target 518
r 0.46920000000000001
]
edge [
source 510
target 524
r 0.4229
]
edge [
source 510
target 533
r 0.52500000000000002
]
edge [
source 510
target 558
r 0.41520000000000001
]
edge [
source 512
target 522
r 0.35100000000000003
]
edge [
source 514
target 538
r 0.36520000000000002
]
edge [
source 514
target 523
r 0.38329999999999997
]
edge [
source 515
target 516
r 0.3508
]
edge [
source 517
target 527
r 0.35899999999999999
]
edge [
source 517
target 522
r 0.50890000000000002
]
edge [
source 518
target 531
r 0.43130000000000002
]
edge [
source 518
target 533
r 0.63200000000000001
]
edge [
source 518
target 522
r 0.44900000000000001
]
edge [
source 518
target 554
r 0.39419999999999999
]
edge [
source 518
target 558
r 0.42349999999999999
]
edge [
source 518
target 563
r 0.46239999999999998
]
edge [
source 519
target 526
r 0.3609
]
edge [
source 521
target 547
r 0.62160000000000004
]
edge [
source 521
target 525
r 0.49170000000000003
]
edge [
source 521
target 523
r 0.36720000000000003
]
edge [
source 522
target 524
r 0.41770000000000002
]
edge [
source 522
target 533
r 0.41959999999999997
]
edge [
source 522
target 560
r 0.46860000000000002
]
edge [
source 522
target 554
r 0.62829999999999997
]
edge [
source 522
target 558
r 0.43609999999999999
]
edge [
source 522
target 562
r 0.38500000000000001
]
edge [
source 522
target 563
r 0.57709999999999995
]
edge [
source 525
target 547
r 0.502
]
edge [
source 526
target 564
r 0.40500000000000003
]
edge [
source 527
target 557
r 0.39729999999999999
]
edge [
source 531
target 533
r 0.53359999999999996
]
edge [
source 531
target 563
r 0.40870000000000001
]
edge [
source 533
target 554
r 0.36030000000000001
]
edge [
source 533
target 558
r 0.38469999999999999
]
edge [
source 533
target 563
r 0.4078
]
edge [
source 536
target 561
r 0.38700000000000001
]
edge [
source 536
target 564
r 0.41110000000000002
]
edge [
source 544
target 548
r 0.45639999999999997
]
edge [
source 553
target 564
r 0.40760000000000002
]
edge [
source 554
target 558
r 0.48259999999999997
]
edge [
source 554
target 563
r 0.55840000000000001
]
edge [
source 558
target 563
r 0.41820000000000002
]
edge [
source 561
target 564
r 0.37509999999999999
]
]

regards


(Evan Bolyen) #5

Hey @1621447326,

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?


(Michael Shaffer) #6

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.

Mike


#7

Hello @michael.shaffer,

I have similar problem.

I followed your tutorial except that I did not do the “qiime SCNIC sparcc-filter” step. I use Cytoscape 3_7_0 in Mac.

Any suggestions? Thanks.


(Michael Shaffer) #8

Hello @eDNA,

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.

Mike


#9

Hi Mike @michael.shaffer,

The network showed up after I clicked the refresh button. I will filter my data and re-run the commands.

Thanks a lot for your help!