Cannot see enrichment map using the string enrichment in cytoscape

[monika chongtham]

Hi,

I wanted to visualise the enrichment map of a network I extracted from string in cytoscape version 3.8.2

I have downloaded all necessary apps for visualising enriched pathways apart from the GSEA. In the toolbar symbol to run enrichment , everytime I click it, I can see the map at the background but there seems to be some kind of partition task, cytoscape gets stuck at.

I do not know how to get past this step.

Please let me know what to do. Attached is an image showing the task where cytoscape gets stuck (in the lower right you can see that the enrichment map is generated). I sincerely hope someone will reach out to me.

Best,

Monika

[Mike Kucera]

Hi Monika,

Can you please provide more detail on the steps you are taking to get to that point?

Thank you.

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[monika chongtham]

Hi Mike!

I don't know if you got my previous email but just resending it.

These are the following steps.

1. Load data (gene list) to STRING

2. Export STRING network to cytoscape

3. Analyze Network

4. Retrived Functional Enrichment

5. Click the Enrichment Map logo in the STRING enrichment in the lower panel (EnrichmentMap App previously downloaded)

And then the output/picture attached previously comes in display and cytoscape gets stuck.

Thanks a lot for any advice,

Monika

[Pradeep Eranti]

Hi Monika and everyone,

I am facing the same issue currently. 

I extracted the STRING network using 300 genes of interest in Cytoscape -> Retrieved Functional Enrichment -> Create Enrichment Map. 

The process is running for the last 20 hours. Is this an error? How much time does it take to generate the map?

I observed the same issue when I tried the same process for a set of 10 genes. I had to abort it in the end. 

Looking forward to your suggestions.

Many thanks,

Pradeep

[Nadezhda Doncheva]

Hi Monika and Pradeep,

I am one of the stringApp developers and I can reproduce the error. Thanks for reporting it.

I will investigate it and see if I can find out what and when it happens. Actually, the network gets created as can be seen by the red dots in the background, behind the progress bar. However, one cannot see it since a certain task somehow never finishes.

Best wishes,

Nadya

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[Mike Kucera]

Hi All,

This is a bug in EnrichmentMap. I made a change to the menu action so that it always shows the "Create EnrichmentMap" dialog. That action is also run by the command that stringApp uses. That causes the EM dialog to appear before the progress bar dialog disappears, which blocks the progress bar dialog and causes it to stay open, since its a modal dialog it blocks the UI.

I'll have to fix this in EnrichmentMap and create a bug-fix release.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CALkcCTo3FzhsRzc9G%3DD14v%2BfZKkwXteffXmV%3DqeWwC3Oc9S1UQ%40mail.gmail.com.

[Mike Kucera]

Hi Monika and Pradeep,

Can you please try this build of EnrichmentMap before I publish it to the app store:

https://github.com/BaderLab/EnrichmentMapApp/releases/tag/v3.3.3

Just copy the jar file to the CytoscapeConfiguration/3/apps/installed folder.

Thank you.

[Lei Hua]

Hi Monika,

Have you sort it out? 

I think I get exactly the same issue, after retreive functional enrichement using STRING enrichment app, then Creat Enrichmentmap from the significant terms, it pops up a window for Creat Enrichmentmap at back and a window of Cytoscape task in the front, it shows the progress of "Partition 4 : Iteration 100 of 100" , it never finishes... although in the network interface, there is a enrichment map, but I can't see it fully.

Best wishes,

Lei

[Pradeep Eranti]

Hi Mike,

After uninstalling the previous version and copying this Github-based jar file, I could confirm that the issue is not faced.

Thanks for the quick resolve.

[Nadezhda Doncheva]

Hi Mike,

I just tested it and I can confirm that things work fine for me as well. Thanks for the quick fix!

Best wishes,

Nadya

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/ba22aa90-00e2-4a46-b380-cabe1c332bfbn%40googlegroups.com.

[Mike Kucera]

Thank you both for testing it. I'll upload version 3.3.3 of EnrichmentMap to the App Store today.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/CALkcCTqVKZh84k-Y1CpsQGUHbHpY3GNVKtT%3DfC0MQxTQfcSveg%40mail.gmail.com.

[monika chongtham]

Hi Everyone and Mike,

Thanks a lot. I couldn't follow up the link before, but I tried now and it works..YAAAY!

I am new to cytoscape, so I was wondering if you know how to change the colour and font size for the enrichment map?

In the attached figure, I want to change the colour and size of the red nodes and make the GO terms more visible. How can I acheive this?

Best,

Monika

[Scooter Morris]

You should be able to change things by using the Style Tab in left-hand panel.  Node Fill Color and Node Label Size will allow you to adjust things.  There is a good tutorial on all of this at tutorials.cytoscape.org -- look for the Basic Data Visualization.

-- scooter