edge import values not brought in

[Paul Benton]

Dear all,

I'm trying to import a simple correlation matrix into cytoscape to view it as a network. It seems that there is no way to import a simple correlation matrix so I have made an edge list, a node attribute file and finally an edge attribute file. I have the network edge list import finally working and I've got the node attributes loading in a numerical pval for the nodes. However, importing the rho value for the edges is becoming difficult. The file imports without errors shows the new column in the edge view but it complete blank. I've tried import this as a floating point and a string just incase. My file looks as follows ( in a tsv format dim of [1345, 2])

A0JNY3 pm Acetate adduct of LysoPC(17:1) -0.916181784511709

A1L2Z3 pm Acetate adduct of LysoPC(17:1) -0.766497080724715

A2A5N2 pm Acetate adduct of LysoPC(17:1) -0.99988747418072

A2A813 pm Acetate adduct of LysoPC(17:1) -0.985939577785385

A2AL50 pm Acetate adduct of LysoPC(17:1) 0.422634142370668

I can manually add values to the rho column after the file has been imported but not from the file. Any help on what I'm doing wrong would be very helpful.

Best,

Paul

[Tim Hull]

Can you send a screenshot of what the table import dialog and the edge table look like? Also, might you have an example data set you can share that will demonstrate the problem?

Tim

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[Paul Benton]

Hi Tim,

Sure. I've attached two different screen shots. One is the import of the edge attribute file (edg) file with cytoscape version number and the other is after the import. You can see from the second screen shot that the rho column is blank, but the file loaded without errors.

A smaller version of the data is in the following dropbox folder: https://www.dropbox.com/sh/jbjb5i21bcno9rw/AADSFY7ZmxfpiklzBSLlumooa?dl=0

Let me know if you need anything else.

Cheers,

Paul

On Monday, April 20, 2015 at 10:16:17 AM UTC-7, Tim Hull wrote:

Can you send a screenshot of what the table import dialog and the edge table look like? Also, might you have an example data set you can share that will demonstrate the problem?

Tim

On Sat, Apr 18, 2015 at 4:47 PM, Paul Benton <hpbe...@gmail.com> wrote:

Dear all,

I'm trying to import a simple correlation matrix into cytoscape to view it as a network. It seems that there is no way to import a simple correlation matrix so I have made an edge list, a node attribute file and finally an edge attribute file. I have the network edge list import finally working and I've got the node attributes loading in a numerical pval for the nodes. However, importing the rho value for the edges is becoming difficult. The file imports without errors shows the new column in the edge view but it complete blank. I've tried import this as a floating point and a string just incase. My file looks as follows ( in a tsv format dim of [1345, 2])

A0JNY3 pm Acetate adduct of LysoPC(17:1) -0.916181784511709

A1L2Z3 pm Acetate adduct of LysoPC(17:1) -0.766497080724715

A2A5N2 pm Acetate adduct of LysoPC(17:1) -0.99988747418072

A2A813 pm Acetate adduct of LysoPC(17:1) -0.985939577785385

A2AL50 pm Acetate adduct of LysoPC(17:1) 0.422634142370668

I can manually add values to the rho column after the file has been imported but not from the file. Any help on what I'm doing wrong would be very helpful.

Best,

Paul

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[Tim Hull]

It looks like the edge identifiers in the table you're importing aren't matching up exactly with the edge identifiers in the network. In particular, I noticed that in the edge attributes file, pm is not surrounded by parentheses in the first column, whereas it is in the network's edge table.

Can you edit the edge table file such that the identifier values are exactly the same as those in the network and try again? This should resolve the issue, unless there is some other kind of mismatch between the table being imported and the identifier in the network. 

Let us know if that fixes the problem...

Tim

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[Paul Benton]

Yep looks like I found out the issue. The edge attribute file has to have the brackets around the interaction although this is not needed for the network file. I guess cytoscape put these in. 

Thanks for the help, wouldn't have thought of looking there as there was a perfect match in the files.

Cheers,

Paul