If you specify a p-value other than the default the legend shows the default and not the value entered in the user interface

Merge two clusters
sort the table
select a new cluster by selecting a section in the network (not by clicking on its name in the annotation table)
Automatically selects name in the annotate table that is different from the one that was selected.

It does not support Expression Set, Intersection, User Defined .. etc

It is currently not possible to load consecutive enrichment maps. Loading a map after launching the app works, but any more attempts after the initial one will result in a null pointer exception being thrown.

Enrichment Map v2.0 Build:400
Cytoscape 3.1.1
Windows7

After I completes my GSEA run, I clicked on Enrichment Map Visualization, set all parameters and clicked Build Enrichmant Map, then Cytoscape was launched but nothing was shown on the Cytoscape. I just got a black screen. Then I tried it the old way by Apps > Enrichment Map > Create Enrichment Map > choose GSEA, in Expression box, choose the .rpt file of the GSEA result > Build. And I got this warning:

What is this warning telling me? What did I do wrong?

Thanks so much in advance for you your help.

Can be fixed by changing the name.

If the post analysis set has the exact same name as one of the nodes in the network its post analysis visual style dominates.
should be one node. if the post analysis node has the same name as a node in the network then its name should be annotated with PA_ (and error message should be issued to let user know).

Hello,

There is some truncated text in the user guide regarding gene expression files:

Gene sets are filtered based on the genes present in the expression file. For example, if Geneset X contains genes

Network is not created when trying to build an enrichment map with just a gmt file

There is no access from the visual mapper to the edge colour/node color/node shape of the post analysis edges so people can't customize it. (post analysis visual style mapping is done through visual mapper bypass instead of creating or modifying existing visual style.)

Need to put it into the EM visual style or create a new visual style (clone original and add new details to it)

When you click on any of the fields in heatmap panel, the panel doesn't sort the heatmap accroding to that column.

When the Mann-Whitney U Test is being performed on enriched gene sets and signature gene sets:
A one-sided test should be done on all gene sets that are either up-regulated or down-regulated. A two-sided test should only be done on gene sets that registered no change in expression.

When I perform automatic annotation, select a cluster and click on the "extract" button, I get an error:

Argument: 'nodesToUse isn't applicable to command: 'wordcloud create'

Then nothing happens.

Cytoscape 3.2 BETA1
EnrichmentMap 2.0.2

Bingo files created in 2.8 work but not bingo files that were created in 3.0

java.lang.ArrayIndexOutOfBoundsException: 1
at org.baderlab.csplugins.enrichmentmap.parsers.EnrichmentResultFileRead
erTask.parseGenericFile(EnrichmentResultFileReaderTask.java:359)
at org.baderlab.csplugins.enrichmentmap.parsers.EnrichmentResultFileRead
erTask.readFile(EnrichmentResultFileReaderTask.java:219)
at org.baderlab.csplugins.enrichmentmap.parsers.EnrichmentResultFileRead
erTask.parse(EnrichmentResultFileReaderTask.java:143)
at org.baderlab.csplugins.enrichmentmap.parsers.EnrichmentResultFileRead
erTask.run(EnrichmentResultFileReaderTask.java:973)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.inne
rRun(JDialogTaskManager.java:337)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(
JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:44
1)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExec
utor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor
.java:908)
at java.lang.Thread.run(Thread.java:662)

When you set the limit of common genes to for example 14 and then click on the edge produced the heatmap show only 6 genes but when you look at the list of genes associated with the edge in the edge browser there are 14 genes listed.

common genes between the Genesets and the post analysis set are being calculating on the original geneset without restriction to the expression set being used for the EM. This generates number based on the absolute overlap instead of what is represented in the EM. When you click on the edge though the expression viewer will only show you the genes that overlap between the two sets that are in the expression set.

Results from great web interface differ from the enrichment maps generated using similar thresholods. The website by default filters by Region fold enrichment greater than 2.

Add ability to filter by one of the fold enrichment terms (region or gene or combination)
Let user set the threshold to filter by
Add option to get rid of terms that don't pass or just change the opacity of those that don't pass.

Reload throws a Null pointer and AutoAnnotateParameters line 113.

Hello,

I'm creating an enrichment map using generic enrichment analysis results. I'm inputting three files: GOBP geneset GMT, and two enrichment result text files. I'm seeing two edges (green and blue) between each fully coloured node. I understand that each colour maps to a different dataset, but if I understand correctly the gene overlaps for geneset A and geneset B will be the same for both datasets since I'm using only one GMT file and generic result files. Also, the enrichment of a geneset in a dataset is represented by the colouring of the core and outer circles of the nodes so the extra edges and the edge colours themselves seem to be unnecessary.
Is there a way for me to not have dataset specific edges?

Cytoscape 3.2.0 beta1
EnrichmentMap 2.0.2

Hi,

I am trying to make my Enrichment Map with the annotation feature. As the instruction, I double clicked the name and typed the new name on it, but it can not be changed after I pressed Enter. Which step I did wrong?

Thanks.

suggested enhancement:

1. be able to get the Binomial and Fisher FDR values ('and' relationships , 'or' relationships by putting one cutoff to 1)
2. be able to enter low (lower than 0.001) values in the parameter boxes
3. be able to play effectively with the pvalue and qvalue slidebars (e.g. by replacing them by -log10(values)
   (4) issues from GREAT: be able to select only the the GO and pathways terms)

Thanks a lot, Veronique.

It is not possible to change the parameters settings to rerun the overlap of the signatures twice on the same session. A "source node is not a member of this network" error appear.

What I'm trying to do is to try different thresholds for example, I try number of common of genes = 1 and then realize that there are too many overlaps and then I try hypergeometric = 0.05, etc,, To do in Cytoscape 2.8 , I delete the signature nodes ( triangle) and related edges and rerun the post-analysis. Here the error (source node is not a member of this network) appears when I hit the "run" button twice.

ERROR LOG AND ENRICHMENT MAP VERSION BELOW:
Cytoscape 3.1.1 EnrichmentMap 2.0.1 build 478 java6

java.lang.IllegalArgumentException: source node is not a member of this network
at org.cytoscape.model.internal.SimpleNetwork.addEdgeInternal(SimpleNetwork.java:265)
at org.cytoscape.model.internal.CyRootNetworkImpl.addEdge(CyRootNetworkImpl.java:254)
at org.cytoscape.model.internal.CySubNetworkImpl.addEdge(CySubNetworkImpl.java:149)
at org.baderlab.csplugins.enrichmentmap.task.BuildDiseaseSignatureTask.buildDiseaseSignature(BuildDiseaseSignatureTask.java:444)
at org.baderlab.csplugins.enrichmentmap.task.BuildDiseaseSignatureTask.run(BuildDiseaseSignatureTask.java:707)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
at java.lang.Thread.run(Thread.java:680)

The Rank sum test incorporated library inflates the jar. Look into calculating the rank sum without having to include the library.

A way around it is make sure the heatmap is set to no sort prior to auto annotating.

Not sure why deadlock occurs sometimes but not others.

Is it a possible to implement a slide bar for the parameters "number of common genes and hypergeometric test" ? : a slide bar that would be similar to the similarity cutoff slide bar but for the "pink" edges.

What I'm trying to do is to try different thresholds for example, I try number of common of genes = 1 and then realize that there are too many overlaps and then I try number of common genes = 5, etc.., To do it now , I delete the signature nodes ( triangle) and related edges and rerun the post-analysis. A slide bar would be more convenient for example to identify the pathway with the best overlap significance.

Thanks a lot
Veronique

on stored session universe is different (if sliders were used to filter genesets in the original anlaysis) which changes the p-values.

In original session all genesets in the initial created EM are used to calculate genes in the universe (even if some have been filtered out) In restored session on genesets present in the map are used making the universe smaller, making the p-values larger.

Will be resolved once universe parameter is calculated on load and stored with session separately.

java.lang.NullPointerException
at org.baderlab.csplugins.enrichmentmap.actions.EnrichmentMapSessionActi
on.handleEvent(EnrichmentMapSessionAction.java:81)
at sun.reflect.GeneratedMethodAccessor79.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAcces
sorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.cytoscape.event.internal.CyListenerAdapter.fireEvent(CyListenerAd
apter.java:120)
at org.cytoscape.event.internal.CyEventHelperImpl.fireEvent(CyEventHelpe
rImpl.java:84)
at org.cytoscape.session.internal.CySessionManagerImpl.setCurrentSession
(CySessionManagerImpl.java:268)
at org.cytoscape.task.internal.session.OpenSessionTask$OpenSessionWithou
tWarningTask.changeCurrentSession(OpenSessionTask.java:184)
at org.cytoscape.task.internal.session.OpenSessionTask$OpenSessionWithou
tWarningTask.run(OpenSessionTask.java:160)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.inne
rRun(JDialogTaskManager.java:337)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(
JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:47
1)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.
java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor
.java:615)
at java.lang.Thread.run(Thread.java:745)

filtering a network by an attribute which has multiple selection belonging to multiple auto annotation groups causes cytoscape to go into an infiinte loop or deadlock situation.

Can only recover by forcing cytoscape shutdown.

Enrichment Map: EnrichmentMapPlugin_v2.0-Beta3.zip (v2.0 Beta build 367)
OS: Windows XP 64-bit
Cytoscape: v3.1.0 64-bit

Install from archive from app manager returns "No manifest was found in the jar file." Install fails.

Hi,

I generated Heat Map (Nodes). When I used "Export Expression Set (PDF)" to export the Heat Map, nothing happened. Is this the right way to export Heat Map image?
Thanks.

Jian

on stored session universe is different (if sliders were used to filter genesets in the original anlaysis) which changes the p-values.

In original session all genesets in the initial created EM are used to calculate genes in the universe (even if some have been filtered out) In restored session on genesets present in the map are used making the universe smaller, making the p-values larger.

Will be resolved once the universe is calculated at build and stored as a parameter associated with each dataset.

Originally submitted by Daniele:

Currently, the GMT used to generate the enrichment map is used as universe-set for the post-analysis Fisher's Test. Ideally, the universe used should be an intersection of the EM gene-sets universe and the query set universe.

However -- since 1) it is not possible to infer the universe unless the users uploads a complete collection of query sets (i.e. an entire database), 2) most of the users would not be able to correctly interpret the request for a universe set, or may have no access to the true universe, or may have no access to this piece of information -- we decided that we should implement the upload the query set universe only as an advanced option.

Additional comments:
Universe can be set to
gmt
expression set
gmt/expression intersection
user defined

distinct expression sets by dataset is not working.
if the files are equal there should be only one edge type.

After creating a second map
Go back to first map
delete post analysis edges originally created
Try and re-run post analysis (without re-specifying the gmt file) and get a "No signature Genesets selected" error.

Error msg isn't sent through the task. It is sent through the ui thread which causes a deadlock.

Error:"Please select at least two clusters" but user can't click on OK because control is to the task.

we were not able to create a map with 2 datasets with Cytoscape3.1.1.
Results are from GSEA preranked that we uploaded using the rpt file.

If none of the enrichment results pass the defined threshold EM will go on to build a network with all the genesets.

Selecting 3 annotated clusters only merges two. Trying to merge the third cluster to the previously merged cluster doesn't work.

Cytoscape 3.2.0 beta1
EnrichmentMap 2.0.2

I am using cytoscape version 3.1.1 and enrichment map version 2.0.1. I created an enrichment map using the David panel. Once the map was obtained, according to the tutorial page here (http://www.baderlab.org/Software/EnrichmentMap/Annotation), for automatically annotating clusters, I am not able to find the option 'Annotate clusters' under Enrichment Map. Please let me know if I am missing something in terms of software versions.

Multiple datasets do not show up when a 1+ dataset enrichment map is loaded in the app and another enrichment map is already present. There must be a problem with how the panels are being updated.

Hi,

I am learning to make my Enrichment Map. How can I remove the individual GO number and annotation from nodes?

Thanks.

When there are no genes associated with enrichment line enrichment results are truncated or don't exist depending on where the empty gene fields occurs.

When building an EM with two generic datasets it crashes with an error that it can't find a geneset eventhough the map can be created if it is only using one of the sets.