Vertex Color Error

Feb 22, 2009 at 9:20 PM
Hi:  I am having trouble getting my verticies to show up as anything but red.  I can change size and opacity based on athe autofill columns tool, but when I change the color of my verticies all show up as red.  In the color field I see a series of three numbers separated by commas (as if they are indications of blue, yellow, red combinations), and there is a little green triangle in the upper left cornor of each cell indicating an error.  If I manually change the color then re-read the workbook, the error recreates itself instead of reading the manual changes. Can someone provide a suggestion about how to fix this?  thanks!
-New NodeXL user
Feb 25, 2009 at 3:23 PM
Hello, JN:

You can ignore those green triangles.  It's just Excel pointing out that the cell contents are not one of the color names in the color drop-down, but the numeric colors entered by the AutoFill Columns feature work fine nonetheless.

I'm not sure I understand the problem you're encountering.  Does AutoFill Columns successfully set the vertex color the first time you use it, but then stops working when you manually enter colors in the Color column?  Or by "change the color," do you mean that you clicked the Options button in the Vertex Color column in the AutoFill Columns dialog box and set some vertex color options?  If you could list the steps you're following, I'm sure I can figure out what's going on.

(By the way, all selected vertices are red by default.  You're not selecting all the rows in the Vertices worksheet, seeing red, and concluding that something is wrong, are you?)

-- Tony
Feb 25, 2009 at 3:39 PM
Thanks for your reply Tony.  I've become increasingly frustrated that NodeXL is not doing what I ask.  The problem is likely user error, but I'm now at a loss for figuring out what I've done wrong, and I'm very grateful for the help.  I have a large dataset with more than 95,000 edges and 438 vertices.  Here are my steps.

I open my data in NodeXL.  While in the Vertices worksheet, I click on AutoFill columns on the left side of the NodeXL ribbon.  I set Vertex Color to a continuous variable I have called "term," where smaller values will appear light gray and larger values will appear black.  I set vertex shape to a dichotomous variable I have called "leader," where 1=solid triangle.  I set vertex radius to a continuous variable called "centrality" where smaller numbers will be smaller radius.  Then I click "read workbook" in the "Document Actions" pane.

While waiting for the graph to be made, the workbook fills in.  However, in the color field, there are series three numbers.  None of the nodes in the graph have appeared in a color I selected.  Even under the "options" button in the "Document Actions" window I've set it so that black would be the default and selected nodes and edges would appear yellow instead of red (which they do).  However, all nodes in the graph appear RED.  In addition, while the workbook correctly filled in the shape field to be equal to "solid triangle" for those who are leaders (=1), there are NO triangles in the graph at all.

Perhaps I don't understand NodeXL's order of operations?  Perhaps I need to uninstall and reinstall?  Any advice and information is appreciated.

-Jennifer
Feb 25, 2009 at 4:04 PM
Jennifer:

No, please don't uninstall and reinstall.  This isn't an installation problem.

If I understand your post, there are two problems:

1. All the vertices appear red in the graph.  You're expecting them to range from light gray to black.

2. The graph has none of the solid triangles you're expecting.

One thing that will cause both problems is if you've used NodeXL's cluster feature.  Is the Show Clusters checkbox in the Analysis group in the NodeXL ribbon checked?

-- Tony

Feb 25, 2009 at 4:55 PM
Great.  Performance is improving.  This fixed a few problems (although I don't understand why exactly).

However, I seem to have a new problem.  I started changing some other features in the worksheet then hit "read workbook" again.  Now I'm getting an error that says "An unhandled exception occurred in your application.  Contact your administrator or the author of this document for further assistance."  My only solution is to close the program and re-open.  But this has happened twice.

-Jennifer
Feb 25, 2009 at 5:27 PM
Jennifer:

"Unhandled exceptions" are program bugs that shouldn't occur.  If you get another one, can you please press Control-C to copy the exception text to the clipboard, then post the text here?  Any details you remember about what you were doing at the time will help me track down the bug.

Thanks,
    Tony
Feb 25, 2009 at 5:32 PM
Here is the error I am getting.  If you can tell me how to avoid this so I can complete my task, I would be incredibly grateful!

A problem occurred while laying out the graph.

************** Exception Text **************
System.InvalidOperationException: A problem occurred while laying out the graph. ---> System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown.
   at Microsoft.NodeXL.Core.Edge.get_Vertices()
   at Microsoft.NodeXL.Core.EdgeUtil.EdgeToVertices(IEdge edge, String className, String methodOrPropertyName, IVertex& vertex1, IVertex& vertex2)
   at Microsoft.NodeXL.Layouts.FruchtermanReingoldLayout.CalculateAttractiveForces(ICollection edgesToLayOut, Single k)
   at Microsoft.NodeXL.Layouts.FruchtermanReingoldLayout.LayOutGraphCore(IGraph graph, LayoutContext layoutContext, BackgroundWorker backgroundWorker)
   at Microsoft.NodeXL.Layouts.AsyncLayoutBase.BackgroundWorker_DoWork(Object sender, DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.OnDoWork(DoWorkEventArgs e)
   at System.ComponentModel.BackgroundWorker.WorkerThreadStart(Object argument)
   --- End of inner exception stack trace ---
   at Microsoft.NodeXL.Visualization.Wpf.NodeXLControl.AsyncLayout_LayOutGraphCompleted(Object oSender, AsyncCompletedEventArgs oAsyncCompletedEventArgs)
   at Microsoft.NodeXL.Layouts.AsyncLayoutBase.FireLayOutGraphCompleted(AsyncCompletedEventArgs oAsyncCompletedEventArgs)
   at Microsoft.NodeXL.Layouts.AsyncLayoutBase.BackgroundWorker_RunWorkerCompleted(Object sender, RunWorkerCompletedEventArgs e)
   at System.ComponentModel.BackgroundWorker.OnRunWorkerCompleted(RunWorkerCompletedEventArgs e)
   at System.ComponentModel.BackgroundWorker.AsyncOperationCompleted(Object arg)
   at System.Windows.Threading.ExceptionWrapper.InternalRealCall(Delegate callback, Object args, Boolean isSingleParameter)
   at System.Windows.Threading.ExceptionWrapper.TryCatchWhen(Object source, Delegate callback, Object args, Boolean isSingleParameter, Delegate catchHandler)

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Feb 25, 2009 at 5:41 PM

It looks like you don't have enough memory in your machine to handle the large graph you're attempting to render.  95,000 edges is a lot of edges, so this doesn't surprise me.

Here are some things you can try to fix the problem:

1.  Close other programs while running NodeXL.

2.  Use Excel's table filtering to filter out some of the edges.  Click on the down-arrow button at the top of each table column to see the available filters.

3.  Add more memory to your machine.

-- Tony

Feb 25, 2009 at 7:26 PM
Thanks Tony, I'm really making great progress now (thanks to you).

Perhaps this question should be in a different thread, but can you tell me how I can tell NodeXL to only include the edges that connect the vertices that appear on the graph?  I want it to exclude all edges that connect to vertices that are not on my graph.
Thanks again,
Jennifer
Feb 25, 2009 at 8:56 PM
Jennifer:

It depends.  What action did you take to cause some of the vertices to not appear in the graph?

-- Tony
Feb 25, 2009 at 11:52 PM
I used a filter in the verticies worksheet.
Feb 26, 2009 at 3:34 PM
1. Invert the vertex filter you're using.  If the filter was ColumnName >= 5, for example, change it to ColumnName < 5.

2. In the newly filtered vertex list, set Visibility to "Skip (0)".

3. Clear the vertex filter.

Now every vertex that you don't want in your graph will be skipped, along with any edges connected to them.

-- Tony
Feb 26, 2009 at 4:00 PM
Ahh, good idea.  Except that I want the "edges" to disappear not the vertices.  The verticies are in fact already filtered and don't appear in the graph.  I just have a bunch of edges that go to verticies that don't exist (if that makes sense).  If, when I filter the verticies, the edges associated them disappears on the edgelist worksheet, your suggestion would work.  But as I see it, when I filter the verticies, all the edges still appear.  I can change the "visibility" column in the edge worsheet manually, but it takes a while to get through them all.

--Jen
Feb 26, 2009 at 5:02 PM
I don't know how to do that.  Perhaps someone else has a suggestion.

-- Tony
Mar 2, 2009 at 5:33 PM

I just wanted to close this thread and say thanks to Tony.  When I started this thread I was ready to give up on NodeXL and try a different software.  But you got me through the big hurdles and I was able to make two really GREAT graphs for a paper that is now under review.  And now I'm going to use NodeXL for a different project.  So, thanks for helping me out and getting me turned in the right direction on NodeXL.  I'm sure I'll be posting to this list again in the future.

 

Regarding the last piece of this thread, I was able to fix my problem by  manually selecting the edges that I needed.  It took a bit of time to go through all the edges manually, but I did it systematically and it only took a few hours.  It really improved the graph.  Thanks again!

 

-Jennifer