Unable to make enhanced graphics work for circos

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Saad Khan

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Nov 18, 2024, 1:11:32 AM11/18/24
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Hi,

I am trying to make enhancedgraphics app work with the following data. Its a ligand receptor plot of clusters (senders and receivers) and on top of that I am making a circos plot around each node. But I am unable to make it work. It would be great if you can correct me what I am doing wrong?sender_reciver_cluster_nodes (1).csv

Ideally on top of each node I would want to make a doughnut (or circos plot) with sender celltype (count) and receiver celltype count but I am unable to make it work. Can you point me in the right direction with regards to this?

Thank you!

Scooter Morris

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Nov 21, 2024, 9:14:34 AM11/21/24
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OK, I was able to get this to work.  I think the problem is that your sender_celltype and receiver_celltype columns aren't actually lists.  They need to be lists of integers to make this work correctly.  Your circoschart string is correct, but I had to do a fair amount of massaging to get the right import.  Note that to import a list of integers, the syntax is 1|2|3| ... (i.e. an integer separated by a verticle bar).  You need to specifically tell the importer that that column is a list of integers also.

-- scooter

Saad Khan

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Dec 9, 2024, 12:04:00 PM12/9/24
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Sorry, I did not check back with you. Can you send me the session file that worked for you?

Thank you

Saad Khan

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Dec 9, 2024, 3:52:25 PM12/9/24
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For some reason I am not able to make it work in list mode either.
Here is another file and what it looks like.

I keep seeing this error in my cytoscape task history not sure if this is related or not.

  •  Column 'celltype_prop' exists in another network and is preventing it's creation here -- skipping column
    •  Column 'celltype_prop' exists in another network and is preventing it's creation here -- skipping column
      •  Column 'celltype_prop' exists in another network and is preventing it's creation here -- skipping column
        •  Column 'celltype_prop' exists in another network and is preventing it's creation here -- skipping column
          •  Column 'celltype_prop' exists in another network and is preventing it's creation here -- skipping colum               
Cluster Adjacency default node.csv

Saad Khan

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Dec 10, 2024, 2:23:16 AM12/10/24
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Nevermind got it to work, But can't adjust size of circos plot

Saad Khan

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Dec 10, 2024, 2:23:40 AM12/10/24
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i.e. vary the size of circos plot by node size.

Scooter Morris

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Dec 11, 2024, 8:42:43 PM12/11/24
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Look at the node visual property: Size->Fix custom graphics to node size and make sure that's checked.

-- scooter
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