can not import a table from file

[宋思扬]

Hi,
I can not import a table from file, Cytoscape show me the word 'types of selected for tables are not matching’. I am not sure if it is about the problem of my mac system.
Because when I use another computer which system is windows xp it is fine. And I import the same kind of excel. What can I do ?

Thanks

[Tim Hull]

Can you give more details as to what exactly you did that triggered the error? Any example files that demonstrate the problem would also help.

Tim

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[Sherwin Kuah]

Hello all,

I've also experienced the same issue as above, with my Cytoscape 3.2.0 and running on MacOS X.

It occurred after importing my network from file. When I import "table from file", "Importing table as: Node table columns", the error message pops up (message reads: "Types of keys selected for tables are not matching".

I have attached the file that demonstrated the problem.

Thanks in advance!

Sherwin

[Tim Hull]

The issue is that the NodeID column contains numbers, and as such is imported by default as a numeric column. The default key column for networks is shared name, which is always stored as a String regardless of the type of data stored. 

If you're using shared name as your key, you'll need to manually change the type of NodeID to a String - to do that, right-click the column header in the table import dialog and change the type from Integer to String.

Hope this resolves the issue - let us know if you're still having problems after trying that...

Tim

[ahmad sofyan]

Hi Tim Hull,

I found new trouble. I succeed importing table real edge table txt, real node table txt (both of table was generated by QIIME).
Previously, when I import edge table, and node table, it got notice "type of selected for tables are not matching". However, I could solve its according your suggestion.

My question is how to generate the visualized network? I have trying to select "layout" but no menus that can be used.
Please give me a suggestion.

Best regards,

Ahmad Sofyan

[ahmad sofyan]

Hi all,

I have similar trouble about importing the table (edge and node) which were generated by QIIME. Previously, I found trouble by notice  'types of selected for tables are not matching’. I could solve its by dirrection from Tim Hull.
Now, my problem is the network could not be seen / visualized ? could anyone give me a suggestion?

Thank you so much,

Ahmad Sofyan 



Pada Selasa, 13 Januari 2015 14.22.14 UTC+9, 宋思扬 menulis:

[Tim Hull]

Are you importing a network, or just the tables? Simply importing a table won't give you a network - you need an actual network file as well.

If you are importing a network file, it may be that the network is very large, in which case Cytoscape won't automatically create a view. In that case, you will see the imported network name in red on the network panel - right-click that and choose Create View in order to create a view.

Let us know if this helps (or not)...

Tim

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[ahmad sofyan]

Hi Tim, 

Thank you very much for your suggestion. Yes, I am successfully in creating a network by right-clicking and choosing "create view". 

My files consisting  1) real_edge_table.txt (25.5 MB), 2) real_node_table.txt (4.6 MB). 3) real_reduced_edge_table.txt (23.7 MB), 4) real_reduced_node_table.txt (3.1 MB). 

I will continue to the further learning with network - interaction in Cystosape 3.2.1. 

Could you give me infomation about

1) what is difference real_edge_table.txt  and real_reduced_edge_table.txt / real_node_table.txt  and real_reduced_node_table.txt  for network analysis using Cytoscape ?

2) I also generate bipartite network files using QIIME (http://qiime.org/scripts/make_bipartite_network.html?highlight=bipartite), and the files generated were 1) EdgeTable.txt, 2) NodeAttrTable.txt, 3) OTUNodeTable.txt, 4) SampleNodeTable.txt. Could you explain about that?

Thank you for your kindness, 

Best Regards

Ahmad Sofyan 

Pada Selasa, 13 Januari 2015 14.22.14 UTC+9, 宋思扬 menulis:

[Tim Hull]

Where did these files come from? That's where I would look to find out the differences between the files - I'd suspect the reduced edge/node tables have less data in them, but you really want to find out from the source...

Tim

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[ahmad sofyan]

Hi Tim,

Data were my experiments. I analysed microbes diversity in rumen using MiSeq Illumina. Then I analysis them by QIIME.

Best Regards,

Ahmad Sofyan  

[Tim Hull]

I would look at the documentation for those tools to find out more about the data files they produce...

Tim

[Meghan Chafee]

Hello Tim,

Sorry to revive an old post but I am also failing to import my node table into Cytoscape 3.2 on Mac OSx. I have changed my node name to a string and it still fails, but it does not give me an error so it's difficult to troubleshoot. I do have empty cells in my node table. Would that cause a problem?

Thanks

Meghan

[Tim Hull]

Have you tried Cytoscape 3.3? We fixed several table import-related issues in that release...

Tim

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[Meghan Chafee]

Hi Tim,

I have tried 3.3. The preview is perfect but then only the column headers show up with empty cells. I don't know what more to do. I've loaded tutorial files with success but not mine but they are clean and no errors are thrown. I have empty cells but all the correct number of delimiters between.

Any further advice?

Cheers,

Meghan

[Tim Hull]

Are you sure you're selecting the right ID column in the network under "Node Identifier Mapping Column"?  If so, do you have a file you can share that exhibits this problem?

Tim

[Meghan Chafee]

Hi Tim,

Attached is my lsa network. First I select 'X' as source and 'Y' as target and import. 

Also attached is my node attribute file. I import to a selected network. "Shared name" is selected for the "Key Column for Network" and in the table I set "node" to the key an convert from number to string. 

I click import and the column headers appear but the cells remain empty. 

Thank you so much for looking into this!

Meghan

[Scooter Morris]

Hi Meghan,
    The problem is that there are quotes around your values in X and Y.  These get imported by Cytoscape intact, so then, when you attempt to import your node attributes, which don't have quotes, Cytoscape isn't able to match them.  I edited out the quotes in your file (attached) and everything was able to import without a problem.

-- scooter

[Meghan Chafee]

Thank you so much for that.

I'm working too much right now.