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Author Topic: Hierarchical Clustering Info field  (Read 8402 times)
Takuya
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« on: December 08, 2009, 01:47:23 AM »

I have a question about J-Express 2009.
Is it possible to export Info field (e.g. Info 1) which is displayed in Hierarchical Clustering as text data?
I want to extract only field included in specific cluster.

If there are advice, please teach it.
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Bjarte Dysvik
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« Reply #1 on: December 08, 2009, 12:35:05 PM »

You can not copy only the text field, but there is a way to copy all annotation for selected genes. If you open a Selection Table (under the Data set menu) you can copy the annotation for the selected data from J-Express into for instance Excel (and from there copy only the columns you like). If you point on a certain branch in the J-Express hierarchical clustering, or perform a manual selection by dragging the mouse over the rows, the selection in this window will update.
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Bjarte Dysvik
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« Reply #2 on: December 08, 2009, 12:54:26 PM »

By the way, I added the requirement: "Should be able to export selections in hierarchical clustering" to our feature requirements database.
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Takuya
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« Reply #3 on: December 09, 2009, 05:01:37 AM »

Thank you for your help.
The problem was able to be solved when trying as shown in the content of your message.

But, there is another question.
Is it possible to export info field in the same order as being displayed in Clustering figure?
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Bjarte Dysvik
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« Reply #4 on: December 09, 2009, 10:28:29 AM »

Sorry, I don't think that is possible at the moment. That is why I added the feature requirement. I see the importance of this feature so I'll try to speed up the implementation.
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Bjarte Dysvik
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« Reply #5 on: December 11, 2009, 08:00:52 AM »

Actually I found a way to do this..

Open J-Express scriping (from methods -> scripting -> Python scripting)

Then paste the following script innto the script Editor:

sel = data.getSelectedRows();
inf = data.getInfos();

NN = len(sel);
for i in range(0,NN):
   selrow = inf[sel[NN-1-i]]
   NN2 = len(selrow);
   st = "";
   for j in range(0,NN2):
      
      if j==0:
         st= selrow[j];
      else:
         st=st+"\t"+ selrow[j];
   print st;

Now point on a sub-branch in the hierarchical clustering window to create a selection (this will not work with table-drag selections).
Click run in the script window and annotation for the selected genes should show in the correct order in the script output window.

Bjarte
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Takuya
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« Reply #6 on: December 15, 2009, 01:20:06 AM »

Thanks to your assistance, I was able to export info field data in the correct order.
Thank you very much for your advice.
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