Failed to import table from file (csv/xlsx)

[Anna W]

Hi, 

I'm new to Cytoscape (v3.4.0) and have been trying to import a node table (tried csv and xlsx) but without success. I can import a table as an "unassigned table" but not straight into the node table. The import doesn't show any errors and according to the "Show tasks..." window the import was successful. However, it only imports the column headings; there is no data. 

There seem to be other threads that show this issue but I haven't yet seen a solution to this. 

Hope you can help.  

Thank you, 

Anna

[Barry Demchak]

Thanks, Anna ...

Are you able to send us a small file that demonstrates this?

Barry Demchak -- from my mobile phone

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[Anna W]

Hi Barry, 

I've added an example xlsx file and some screenshots. 

Things I have also tried:

• renaming all the columns either to include or remove "shared name" and "name"
• removing any column titles and unticking in "Advanced Options", "use first line as column names"
  
• created new files and saved them as csv and xlsx before trying to import

Thanks for any help with this. 

Anna

On Wednesday, August 3, 2016 at 1:28:05 PM UTC+1, Barry Demchak wrote:

Thanks, Anna ...

Are you able to send us a small file that demonstrates this?

Barry Demchak -- from my mobile phone

On Aug 3, 2016 4:46 AM, "Anna W" <annaca...@gmail.com> wrote:

Hi, 

I'm new to Cytoscape (v3.4.0) and have been trying to import a node table (tried csv and xlsx) but without success. I can import a table as an "unassigned table" but not straight into the node table. The import doesn't show any errors and according to the "Show tasks..." window the import was successful. However, it only imports the column headings; there is no data. 

There seem to be other threads that show this issue but I haven't yet seen a solution to this. 

Hope you can help.  

Thank you, 

Anna

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[Barry Demchak]

Hi, Anna –

 

Normally, Cytoscape would want to import a network, which would involve each row having a source and target node. Any other values on the row could be source node attributes, target node attributes, edge attributes, or values to be ignored.

 

As you say, the node list in your XLS is just a node list … which could be considered a list of source nodes without target nodes … and with all other values in a row being source node attributes.

 

If I set up the import that way (ID is a source node, name2 & type are source node attributes … see picture below), I get a decent enough network consisting of only nodes with attributes (see other picture below). Is this where you’re trying to go??

 

 

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[Anna Weston]

Hi Barry,

Thank you for your help. At this stage I was just trying to achieve a network of nodes as I wanted to ensure I could get the import function to work. I’ve followed your instructions and that works perfectly! 

I will now create a xlsx file following your advice with each row having a source and target node so that I can start to build a network. 

Thanks again for your help and quick replies. 

Anna

On 3 Aug 2016, at 16:56, Barry Demchak <idekerlab...@gmail.com> wrote:

Hi, Anna –

 

Normally, Cytoscape would want to import a network, which would involve each row having a source and target node. Any other values on the row could be source node attributes, target node attributes, edge attributes, or values to be ignored.

 

As you say, the node list in your XLS is just a node list … which could be considered a list of source nodes without target nodes … and with all other values in a row being source node attributes.

 

If I set up the import that way (ID is a source node, name2 & type are source node attributes … see picture below), I get a decent enough network consisting of only nodes with attributes (see other picture below). Is this where you’re trying to go??

 

<image001.png>

 

<image002.png>

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[Barry Demchak]

Great … good luck!