Merging two networks

[Gaurav]

Hi,

Can someone please help me out in merging two networks using Advance network merging tools?

The main issue is that I am trying to open two networks together in Cytoscape. But it seems like I can only open one network at a time. On opening a network, when I try to open another one, it asks me to close the previous one.

Please assist me in carrying out this work.

Thanks,

Gaurav

[piet molenaar]

Hi Gaurav, 

File>Open is used to open a Cytoscape session file

To import multiple networks during a session you should use file>import

I agree this can be a bit confusing, but a session stores every setting and all networks loaded in one go.

Hope this helps

Piet

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Department of Oncogenomics, M1-131
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[Gaurav]

Hello Piet,

Thanks for your concern.

I tried your suggestion, but somehow it's not working either. I don't know why but Cytoscape only allows to open one network at a time, which is knida frustrating.

Please help if you any other suggestion.

Thanks & Regards,

Gaurav

On Tuesday, July 9, 2013 1:08:39 AM UTC-6, Piet wrote:

Hi Gaurav, 

File>Open is used to open a Cytoscape session file

To import multiple networks during a session you should use file>import

I agree this can be a bit confusing, but a session stores every setting and all networks loaded in one go.

Hope this helps

Piet

On Tue, Jul 9, 2013 at 6:01 AM, Gaurav <kaus...@isu.edu> wrote:

Hi,

Can someone please help me out in merging two networks using Advance network merging tools?

The main issue is that I am trying to open two networks together in Cytoscape. But it seems like I can only open one network at a time. On opening a network, when I try to open another one, it asks me to close the previous one.

Please assist me in carrying out this work.

Thanks,

Gaurav

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[IgorRodchenkov]

Hi Gaurav,

On Friday, July 12, 2013 1:52:15 PM UTC-4, Gaurav wrote:

Hello Piet,

Thanks for your concern.

I tried your suggestion, but somehow it's not working either. I don't know why but Cytoscape only allows to open one network at a time, which is knida frustrating.

I doubt this ;) Because, I can create many network and views in many different ways using different cytoscape versions.

Can you tell us how exactly do you open (or create) a network and then attempt to add (open) another one? Looks, you're still only trying via File->Open...

Which Cytoscape, System, Java?

Igor.

[piet molenaar]

Hi Gaurav,

Did you try to file>import on the two networks in succession? You cannot use file>open to open multiple networks.

If your problems persist, you can send me the files and I'll try to figure out what's wrong. 

Cheers,

Piet

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[Gaurav Kaushik]

I don't know I still got the message by sending large files. I think I am gonna attach both files one by one.

Hope this works.

Apologizes for the inconvenience.

Regards,

Gaurav

On Mon, Jul 15, 2013 at 1:42 AM, Gaurav Kaushik <kaus...@isu.edu> wrote:

Since the total allocated space for 2 networks was >8MB, I am attaching the compressed file (zip) of the folder containing .cys files.

Please have a look, and thanks again for your help.

Best Regards,

Gaurav

On Mon, Jul 15, 2013 at 1:38 AM, Gaurav Kaushik <kaus...@isu.edu> wrote:

Hello Piet and Igor,

Thanks for your concern. 

First of all, I didn't see any option to import a network from .cys file. I can only open it into the Cytoscape (v 2.8.3). And, when I open another file after uploading one file already, it asks me to close the previous one. Sorry, but its a little frustrating since I have to merge two networks using Advance Network Merge tool. 

I am attaching my 2 .cys files (Network_gk 1 and Network_gk 2) for your reference. If possible, can you please merge these networks and send it to me? 

This step of merging is very important for me and I have been trying to do this for ~6 days :(

Please have a look and let me know accordingly.

Thanks & Regards,

Gaurav Kaushik

PhD Candidate

Biological Sciences

Idaho State University

Pocatello Idaho

USA

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[Gaurav Kaushik]

And, here is my second file of my network.

Thanks,

Gaurav

[Gaurav Kaushik]

Hello Piet and Igor,

Thanks for your concern. 

I have sent you guys both files. 

I am sending you my message (below) just to make sure you have received it. I am afraid if googlegroups did not send you my previous mail due to its large size.

Regards,

Gaurav

First of all, I didn't see any option to import a network from .cys file. I can only open it into the Cytoscape (v 2.8.3). And, when I open another file after uploading one file already, it asks me to close the previous one. Sorry, but its a little frustrating since I have to merge two networks using Advance Network Merge tool. 

I am attaching my 2 .cys files (Network_gk 1 and Network_gk 2) for your reference. If possible, can you please merge these networks and send it to me? 

This step of merging is very important for me and I have been trying to do this for ~6 days :(

Please have a look and let me know accordingly.

Thanks & Regards,

Gaurav Kaushik

PhD Candidate

Biological Sciences

Idaho State University

Pocatello Idaho

USA

[piet molenaar]

Hi Gaurav,

What you send me is a session file; this is an entire session including all visual properties and data of the networks in that session. By definition a session file (recognizable by the *.cys extension) can be opened only one time. This is done through the file>open facility. Cytoscape will recognize a session file and won't allow you to open multiple sessions.

If you want to merge networks (with e.g xgmml or sif extension, or from an excel sheet) you have to import these into an instance of a session file using the file>import facility (http://cytoscape.org/manual/Cytoscape2_8Manual.html#Creating Networks).

I've now opened your second session file; saved the network as an xgmml file (file>export>network and attributes as xgmml), closed the session, opened your first session file and imported the network into that session.

Sessions are singular, you can import multiple networks into one session and merge them subsequently.

Cheers,

Piet

[Gaurav Kaushik]

Thanks Piet for your help.

You saved my life :) It worked very nicely and I got my two networks merged into one using SIF extension.

Thanks again for your cooperation.

Best Regards,

Gaurav

[Oriol Guitart Pla]

Hi Mariano,


You are right, K2 only accepts strings columns as input data. The reason
is that Bayesian metrics, used for this algorithm and available in Cyni,
only work with discretized data so the data type needs to be a string.
Basically, these metrics compute probabilities for the possible
combination of input finite values.
If you want to use K2 with your data that contains continuous values,
you could use the Cyni Discretization tools and discretize the columns
in your data. Then you could use these discretized columns to apply the
K2 algorithm.
Regarding the format of the table. If you are not developing new apps
through Cyni, you only need to know that for a new loaded table each row
would be a possible node in a new inferred network and the columns of
that table would be the attributes of that node. For instance, you could
load gene expression data, where each row would represent a gene and
each column an expression value. Then Cyni algorithm would use the
expression values for each gene to try to find connections between the
genes.
Hope it helps,


oriol

[Divya Prakash]

hi,

 i am new in cystoscape can any one help me to select nodes from imported network using another file. 

[Abraian Miller]

Hello Piet,

Each time I do the program reads that it cannot "initialize the preview" so that I can choose the identifier columns. Can you tell me if there is something wrong with my columns or general formatting to resolve this issue? 

[piet molenaar]

Hi, I just succesfully imported your network, find the session file attached.

Did you use File>Import>Network from file?

Regards,

Piet

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Amsterdam University Medical Centers