Cannot import table / node attributes

[zvebbo]

Hello.

 

Quite new to cytoscape.

I have imported a network through import file. I have an .xlsx file with about 7 columns. I choose Source, Interaction, and Target and that works fine.

If I have understood correctly I should then be able to choos Import Table, chose the same file, and have the 4 columns that are left as node attributes (eventhough i only use two for that). The extra columns are added to my Node Table but all the new cells are empty. This is the result if i import directly to my network and also if i import to an unassigned table which i then merge with my network. In the unassigned network all the data is in the cells.

 

I choose column 1 as my Source, then I choose the same column as key when i import the table, is this correct?

Is what I want to do possible?

 

I have also tried with an .attrs file which is looking somewhat like:

NEW_COLUMN_NAME

Source1 = class

Source2 = class

Source3 = class2

etc.

 

Same result there, i get a new column but no data in the cells.

Any ideas that might help me?

 

Bonus question:

If i get my attributes on the nodes, can I then cluster on thos attributes?

[Barry Demchak]

It sounds like you're very close ... can you send us the file you're using?? We're happy to take a look.

[zvebbo]

Hello,

 

thank you for replying and for wanting to help!

I cannot share my files (company secrets) so i made a mock file just to show you what I was doing. Then it suddenly worked!

I realized that the problem was that my node names and attributes were containing spaces and that somehow messed things up. I did try yesterday to put everything in quotation marks but that didnt help.

Anyway, i removed all the spaces and everything is fine now.

 

Thanks again!

[Tim Hull]

Can you share the problematic test file? I wouldn't think spaces should be a problem - that might be a bug somewhere...

Tim

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[Radina Disheva]

Hi guys, I have a similar problem. I have been exploring Cytoscape for only a day, and I can't find a way to import a table to use for a new network. I think I am doing something extremely wrong, but I don't know what it is. I read a lot of stuff, but don't get it.

I created a test network of 4 nodes, and I'm trying to import a very simple .csv file but it only gets in as an Unassigned Table. If I choose any other destination, I don't see the records from the table in the Table Panel.

I sincerely don't know what to do with this Unassigned Table and how to visualize the data in it. 

Sorry for the rookie question, but this is my last resort.

[Scooter Morris]

Hi Radina,
    You need to Import->Network->from File to import a network from a table first.  Once you've imported the network, you can add new tablular data to the network (or create an unassigned table) using the Import->Table->from File.

-- scooter

[Radina Disheva]

Thanks, Scooter, mission accomplished! 

[AR]

See attached video.

One time the files work 6 minutes later (next time) they do not.

Same excel source files.

Other issue...

When the import fails, the file remains locked.  So I have to change file names.  (At this point I have over 100 xlsx files I've tried) with ~ 5 successful imports on the full data set. 

https://drive.google.com/file/d/0BxzPa5ZHy-SRblAydV9nWURCV3c/view?usp=sharing

https://drive.google.com/file/d/0BxzPa5ZHy-SRZUVFWGVhMTNodVE/view?usp=sharing

[AR]

I have been fighting with the exact same problem for the three weeks.  The import is buggy.

1. Sometimes it will work. 

2. Most times loading of the network file fails without explanation.

3. Once an import works, they all work. 

Are their any text delimiters that might make the imports fail?  My data is from a lua database and contains array information and quoteable strings.

AR

[Barry Demchak]

Thanks, AR …

 

This would be much easier to understand with narration or bubbles … it’s hard to watch as it’s moving so quickly but not having an idea of where you’re seeing problems. Can you give us some idea of the timeline, particularly the place you’re trying to draw our attention to?

 

Cool video application … which one are you using?

 

Also, it looks like you’re on Windows 8 … or 8.1 … do you know which it is?? Would you mind running the Troubleshooting script to tell us more about your configuration? http://www.cytoscape.org/troubleshooting.html

 

Thanks.

--

[AR]

Hi Barry,

You resolved the issue by sending me a link for version 3.3 which does not exhibit the same behaviour.

Responses to your questions...

"This would be much easier to understand with narration or bubbles … it’s hard to watch as it’s moving so quickly but not having an idea of where you’re seeing problems. "

Agreed, narration and bubbles would make it much easier. 

"Can you give us some idea of the timeline, particularly the place you’re trying to draw our attention to?"

The timeline was doing an import from start to finish, and Not getting the node data.

"Cool video application … which one are you using?"

 

Software = FastStone Capture, (poor mans version of Camtasia).

  Timeline and node bubbles = Camtasia post processing.  

  Faststone is just straight screen capture, no video editing functionality.

"Also, it looks like you’re on Windows 8 … or 8.1 … do you know which it is?? "

  Windows version 10. With Classic Shell installed.  Classic shell makes it look more like Windows 7, which is good, because it is a work computer. 

"Would you mind running the Troubleshooting script to tell us more about your configuration? http://www.cytoscape.org/troubleshooting.html"

Results from the troubleshooting batch file (from link)

Cytoscape System Requirements Checker for Windows

-------------------------------------------------

Target Cytoscape version: 3.3.0

Your Windows version is:

Microsoft Windows [Version 10.0.10240]

Java is installed

Your system is 64 bit

JAVA_HOME is not set

Your Java version is at least 8.0 as required

Your Java is 64 bit as recommended

The "app" store at apps.cytoscape.org is reachable

Summary

-------

Success! You are ready to run Cytoscape 3.3.0

More details on Java

--------------------

java version "1.8.0_65"

Java(TM) SE Runtime Environment (build 1.8.0_65-b17)

Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)

More details on apps.cytoscape.org

----------------------------------

Going to run trace route command for apps.cytoscape.org with timeout of 30000ms now...

Tracing route to apps.cytoscape.org [132.239.8.176]

over a maximum of 30 hops:

  1    <1 ms    <1 ms    <1 ms  homeportal [192.168.100.254]

  2     *        *

On Monday, November 23, 2015 at 6:32:28 PM UTC-6, Barry Demchak wrote:

Thanks, AR …

 

This would be much easier to understand with narration or bubbles … it’s hard to watch as it’s moving so quickly but not having an idea of where you’re seeing problems. Can you give us some idea of the timeline, particularly the place you’re trying to draw our attention to?

 

Cool video application … which one are you using?

 

Also, it looks like you’re on Windows 8 … or 8.1 … do you know which it is?? Would you mind running the Troubleshooting script to tell us more about your configuration? http://www.cytoscape.org/troubleshooting.html

 

Thanks.

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of AR
Sent: Sunday, November 22, 2015 4:37 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] Re: Cannot import table / node attributes

 

See attached video.

 

One time the files work 6 minutes later (next time) they do not.

Same excel source files.

 

Other issue...

When the import fails, the file remains locked.  So I have to change file names.  (At this point I have over 100 xlsx files I've tried) with ~ 5 successful imports on the full data set. 

 

https://drive.google.com/file/d/0BxzPa5ZHy-SRblAydV9nWURCV3c/view?usp=sharing

https://drive.google.com/file/d/0BxzPa5ZHy-SRZUVFWGVhMTNodVE/view?usp=sharing

 

 

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[Aiman Barki]

Hello AR,

I am trying to use cytoscape. This is my first time. I have no idea what i am doing.  My professor gave me some excel files. What he said to me is the following:

The data under Preterm and Term are the main data and there are a number of cytokines on the left. The cytokines and their relationships are what I’d like to figure out…if they are related, and how, and what it means if one cytokine goes up and a linked one goes up or down…

So can you guide me from where i need to start ?

Thanks

[Barry Demchak]

Hi –

 

Have you tried the tutorials (http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3) or the manual (http://manual.cytoscape.org/en/stable/)? Good information on how to use Cytoscape, but not how to perform specific analyses. For that, you’ll need to go back to your professor.

 

Best of luck …

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Aiman Barki
Sent: Tuesday, March 21, 2017 12:49 PM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] Re: Cannot import table / node attributes

 

Hello AR,

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