Answers.Body: <p>There is two things that you can do.<br />
  First, as Scooter recommended you can update your Style so the node name is mapped to a column that has the pathway name.  (By default, EM uses the GS_Descr because with a lot of the gmt sources the description is better than the name ).
  <a href="https://i.sstatic.net/Z4xXgY7m.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Z4xXgY7m.png" alt="enter image description here" /></a></p>
  <p>Second, EM is actually pulling the pathway description value from the gmt file, the pathway description file.   So if you are doing a lot of analyses with the same gmt file best to update it so that you don't have to change the style every time.  EM isn't looking for a column called GS_descr.  It is using the second column in the gmt file (which is the pathway description).  when creating your gmt file and you don't have pathway descriptions just duplicate the first column and put it in the second column and then your node names will be better.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-21T18:25:07.173Z
Answers.LastActivityDate: 2024-11-21T18:25:07.173Z
Answers.UserDisplayName: Ruth Isserlin
Answers.Body: <p>I haven't seen that before, but there is a simple fix.  You say &quot;the pathway is there&quot; so I assume there is a column with the pathway name.  If so, go to the style panel and change the &quot;Label&quot; to use that column rather than the GS_DESCR column and the pathway name should appear.  Perhaps one of the EnrichmentMap people can provide more information on how that column gets to &quot;NA&quot;</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-11-21T14:23:15.447Z
Answers.LastActivityDate: 2024-11-21T14:23:15.447Z
Answers.UserDisplayName: Scooter Morris
Body: <p>I'm having a difficult time with cytoscape and am wondering if anyone has encountered this issue before. I have several datasets analyzed in R with GSEA for pathway analysis that I'm trying to visualize in cytoscape with Enrichment Map. I've managed to upload my data into the platform and generate clusters of nodes with Enrichment Map, but it displays &quot;NA&quot; for each node point rather than showing the pathway name. When I click on each node, the pathway is there with associated genes and expression data, but GS_DESCR is listed as NA.</p>
  <p>Please correct me if I'm wrong with any of the following, but there doesn't seem to be a way to change what the nodes are called except by manually changing each one which is not a viable solution (there are thousands). I've tried adding a GS_DESCR column manually to my GSEA file; I've made sure to use the same gmt file that generated my GSEA results file so that the pathway names match; I've added descriptions to the expression data file; I've made sure there are no &quot;NA&quot;s in any of the excel files I'm uploading; I've modeled my input files off of an example set (the mesenchymal vs immune cell example on the cytoscape website). All without success.</p>
  <p>Has anyone else dealt with this? What worked?</p>
  
Tags: <cytoscape>
Title: When I upload my data for Enrichment Map, each node displays as "NA"
ThreadText: # When I upload my data for Enrichment Map, each node displays as "NA"
  
  (Asked by: username_0 on 2024-11-20)
  
  I'm having a difficult time with cytoscape and am wondering if anyone has encountered this issue before. I have several datasets analyzed in R with GSEA for pathway analysis that I'm trying to visualize in cytoscape with Enrichment Map. I've managed to upload my data into the platform and generate clusters of nodes with Enrichment Map, but it displays "NA" for each node point rather than showing the pathway name. When I click on each node, the pathway is there with associated genes and expression data, but GS\_DESCR is listed as NA.
  
  Please correct me if I'm wrong with any of the following, but there doesn't seem to be a way to change what the nodes are called except by manually changing each one which is not a viable solution (there are thousands). I've tried adding a GS\_DESCR column manually to my GSEA file; I've made sure to use the same gmt file that generated my GSEA results file so that the pathway names match; I've added descriptions to the expression data file; I've made sure there are no "NA"s in any of the excel files I'm uploading; I've modeled my input files off of an example set (the mesenchymal vs immune cell example on the cytoscape website). All without success.
  
  Has anyone else dealt with this? What worked?
  
  **Tags:** cytoscape
  
  
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  ## 2 answers
  
  ### Answer by username_1 on 2024-11-21. Score: 1
  
  There is two things that you can do.  
  First, as username_2 recommended you can update your Style so the node name is mapped to a column that has the pathway name. (By default, EM uses the GS\_Descr because with a lot of the gmt sources the description is better than the name ).
  [![enter image description here](https://i.sstatic.net/Z4xXgY7m.png)](https://i.sstatic.net/Z4xXgY7m.png)
  
  Second, EM is actually pulling the pathway description value from the gmt file, the pathway description file. So if you are doing a lot of analyses with the same gmt file best to update it so that you don't have to change the style every time. EM isn't looking for a column called GS\_descr. It is using the second column in the gmt file (which is the pathway description). when creating your gmt file and you don't have pathway descriptions just duplicate the first column and put it in the second column and then your node names will be better.
  
  
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  ### Answer by username_2 on 2024-11-21. Score: 0
  
  I haven't seen that before, but there is a simple fix. You say "the pathway is there" so I assume there is a column with the pathway name. If so, go to the style panel and change the "Label" to use that column rather than the GS\_DESCR column and the pathway name should appear. Perhaps one of the EnrichmentMap people can provide more information on how that column gets to "NA"
  
  
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