Import node attribute from table not importing values; Cytoscape 3.2.1

[gabs]

Hi All,

I have tried for the past hour to import node attributes into Cytoscape 3.2.1. 

I am attaching the file here. I would be glad for any help to get this working and reasons why it isn't working.

[Scooter Morris]

Can you give us a little more of an idea of how you are attempting to import the attributes and what isn't working.  Your file looks like it should import just fine, assuming that the first column is the key and it matches a key in your network.  You'll need to make sure that "," is set as a column delimiter and it looks like the middle column is always "=" -- don't know if you really want to import that or not, but you certainly can.

-- scooter

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[David Oliver]

I am also having this problem. Cytoscape loads the new column just fine but it does not contain any data.

[David Oliver]

[SOLVED] I had set the <where to import table data> drop down to "selected network only" and selected my target network but using this option removes the drop down for selecting which target network key value to match the imported data table to. Hope someone else finds this information useful.

[Scooter Morris]

Hi,
    Can you send me a copy of your file, and a snapshot of your node table browser?  That will help me figure out what the problem might be.  By the way, there's also going to be a Cytoscape workshop at UC Boulder next month, if you're interested.  Shelley Copley is hosting it.

-- scooter

On 07/23/2016 01:53 PM, brde...@colorado.edu wrote:

I am having the same problem where the new columns added to my Node Table are empty. I tried the above solution but it did not work. I have tried variations to make sure that there are no hidden characters in my files and that the node names match exactly, but still can not get the information to add properly.  My goal is to color each node by a value, which seems to be most easily done by coloring source and target node via a node table attribute.  Thanks!

On Tuesday, July 21, 2015 at 1:25:41 PM UTC-6, David Oliver wrote:

[SOLVED] I had set the <where to import table data> drop down to "selected network only" and selected my target network but using this option removes the drop down for selecting which target network key value to match the imported data table to. Hope someone else finds this information useful.

On Tuesday, July 21, 2015 at 3:04:12 PM UTC-4, David Oliver wrote:

I am also having this problem. Cytoscape loads the new column just fine but it does not contain any data.

On Monday, April 27, 2015 at 12:09:22 PM UTC-4, Scooter Morris wrote:

Can you give us a little more of an idea of how you are attempting to import the attributes and what isn't working.  Your file looks like it should import just fine, assuming that the first column is the key and it matches a key in your network.  You'll need to make sure that "," is set as a column delimiter and it looks like the middle column is always "=" -- don't know if you really want to import that or not, but you certainly can.

-- scooter

On 04/27/2015 02:48 AM, gabs wrote:

Hi All,

I have tried for the past hour to import node attributes into Cytoscape 3.2.1. 

I am attaching the file here. I would be glad for any help to get this working and reasons why it isn't working.

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[maria.touc...@gmail.com]

Hi!

I have the same problem. I want to add a column with a value to scale the node size with. The table loads fine but the data does not appear in the column on the node table.

These are the top 5 lines of the table I want to import:

medias_x genome
3.18428571428571 X1
2.08571428571429 X2
3.02714285714286 X3
0.795714285714286 X4
0.238571428571429 X5

I was thinking maybe the format of the "medias_x" data, they need to be integers or something specific¿?

Hope somebody can help me out here!

[Scooter Morris]

Greetings,
    I assume you are using 3.6.1, your network has a "name" column that
corresponds to your genome, and you've selected "genome" as the key
column, right?  After you're import, if you click on the "Show Columns"
button (looks like a two-column table) do you see the medias_x column there?

-- scooter

[María Touceda Suárez]

Hi Scooter, 

Yes, you are right about the version and my columns. And yes, when I click the “Show Columns” button the medias_x column is there. But it is empty still. 

María

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[Scooter Morris]

Hi María,
    Can you send me a small session file and your import table?  I'll give it a try here and see what might be going on.

-- scooter

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[María Touceda Suárez]

Here it is. Thanks a lot! 

María

[Scooter Morris]

Hi María,
    Your name field is "1,2,3,4,5", etc., but your input key is "X1, X2,....".  That probably won't work.

-- scooter

On 05/29/2018 08:38 AM, María Touceda Suárez wrote:

Here it is. Thanks a lot! 

María

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[Katherine Wolcott]

Hi,

I am also having the same problem. When I import my node attributes, I am able to see them in the nodes table within Cytoscape, but all of the cells are blank. I imported it to "selected networks only" and the keys match the shared names from my network.

My cytoscape session file and the node attributes table are attached.

Thank you for the help,

Katie

[Scooter Morris]

Hi Katie,

   Your "name" field in Cytoscape is quoted -- i.e. "Begerow", but your CSV file shows the Name as unquoted -- i.e. Begerow.  That's why it's not matching...

--- scooter

[Aswathy S]

Hi,

I am facing a almost similar problem. 

I have created a network based on my gene list using STRING database. Then i tried to load the attribute file for the same, because i want to highlight the common nodes as per the attribute file. But after loading the attribute file, when I checked the Node Table tab, the node values (from attribute file) are not listed there. I assume some problem with the file format or loading . 

Please have a look and help me to find what mistake I did.

I am attaching a sample genelist used for creating network, corresponding attribute file, two screen shots for loading attribute.

Thank you.

Aswathy

[aswat...@gmail.com]

On Thursday, 7 February 2019 20:53:36 UTC+5:30, Scooter Morris wrote:

Hi,

I am also facing similar problem while loading attribute files in cytoscape. First of all i will tell you the steps I followed.

1. I have a list of 100 genes and visualize its interaction based on STRING database. Therefore, I have loaded the gene list in cytoscape using Import->Network From Public Database selecting my organism and I git the networks based on this data. (See sampleGeneList.txt attached)
2.Now I wanted to add an attribute file with geneID and unique/shared (with my other group) info to this network . I have used Import Table from File option . (See sampleAttribute.txt and Figure1.png attached)

But the node vale from the attribute file is not loaded in the Node Table tab. See Figure2.png attached.

Ulimately, I want to visualize the network with shared nodes (Common_AB) from attribute file in one color and highlight the same.

Please let me know what wrong I did in the process.\

Thank you in advance,
Aswathy

[dawn ap]

Hello Aswathy,

I suspect that when String imports the network it uses a different identifier than your original ones. When you attempt to import the attribute it tries to match the key column to the shared name column of the network and they don't match.
For example:
AT4G31985 in the gene list is mathed by String to RPL39A and is then used as node name
so there is no node named AT4G31985, instead it's named RPL39A

Hope this helps!

Dawn

[Aswathy S]

Hi Dawn,

you were right !It was the problem!! Now I loaded my attribute file against query term and I am getting as expected.

Thank you for the help

Aswathy

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