I basically want to capture the network of interactions and nodes defined by a certain parameter and connected in a few ways (by node, and by outgoing as well as incoming connections), so that I can define a sub network of connections.
The problem is that dragging any one of these individual filters to a subfilter spot filters the results further, rather than adding results together (as a Union, "OR") query might.
I can do this manually and within spreadsheets (and then import the results again into Gephi in order to obtain a visualization), but I'm wondering if it's possible to perform a UNION within Gephi, and the steps to take, or the plugin that I might need to do so.
Thanks for your help and continued support. This software is really invaluable.
HDean
Statistics:Posted by hdean83@gmail.com — 05 Sep 2013 15:34
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mbastian wrote:However you can already achieve many things using the new MASK operators. That would let you get the nodes connected to a set of other nodes (the partition nodes) and therefore get the neighbors.
Sorry for the dumb question, but can you explain a bit further how you would do that? I can't find my way around using MASK and neighbors filters. I would like to filter a partition set, then shows all connected neighbors which fulfill some additional condition (degree, partition, etc.), like "what are the biomarkers which are 2nd degree neighbors of these proteins".Eventually, I believe this should be done by a right-click out of any selection, like CTRL-click, rectangle tool etc. I select nodes, then I ask for 1st degree or 2nd degree neighbors. If I need additional constraints on neighbors, that's where I use the filters.
This is basic manipulation, which should be easy to reach.
Thanks
Statistics:Posted by happyconch — 20 Jun 2011 15:38
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Another improvement:
Adding the parameter name + filter name as a query title, for instance "Label Equal" instead of "Equal", "Modularity Class Partition" instead of "Partition". It is really useful when you have 5 filters with the same kind of root, but executed with different parameters!
Statistics:Posted by admin — 19 Dec 2010 21:25
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Besides this, have you watched people using Filters? I'm sure we could learn a lot
And what having icons for filters? The SPI allows itm but we don't use it
Statistics:Posted by mbastian — 19 Dec 2010 19:11
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Duplicate
Sometime we want to change more than one sub-query parameter, and would like to switch easily between the two configurations to see what's going on. This action would not be possible for sub-queries.
Replace by
Example: you create a UNION query, and you just want to see what happens with an INTERSECTION. For the moment you need to build another query in 4 clicks: 1/add the new operator as query, 2/ expand it, 3/ drag the first sub-query, 4/ drag the second one. By selecting "Replace by", a window with the list of possible filter appears.
An alternative is to drag the replacing filter from the library to the _name_ of the replaced filter, holding a key like "Ctrl" to avoid mistakes.
Dragging sub-filters
By the way, when adding a filter as a sub-query, the root must be expanded to drag the filter to the line "Drag subfilter here". I'd prefer to drag it to the name of the root, and see it automatically expanded.
Settings Panel
Finally, the settings panel remains open after removing a query. It should be closed automatically to avoid confusion.
All of this are proposals to discuss of course
Statistics:Posted by admin — 19 Dec 2010 17:24
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Yes it's tricky because you have to add nodes...Removing nodes is a more natural use-case for filters and is easier to handle. But with existing filters as example I think it's okay
Statistics:Posted by mbastian — 16 Oct 2010 15:13
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The HowTo is really easy to handle! Figuring out the difference of merging two set of nodes from the local and main view is more tricky.
Statistics:Posted by admin — 16 Oct 2010 00:08
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For a neighbor filter, one can get inspired from the ego filter code. It wouldn't be difficult to modify it in that way. Follow the tutorial HowTo write a filter.
Statistics:Posted by mbastian — 14 Oct 2010 17:24
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Expanding a selection/filter to the direct neighbors. This way one can for instance:
- select a partition and the in/out connections.
- select two partitions and see the paths linking these partitions at a distance 1
Statistics:Posted by admin — 14 Oct 2010 11:34
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#3: A 'Select All' and 'Unselect All' option is available when you right click on the panel.
The big challenge of 2011 will be to write the manual. 
Statistics:Posted by admin — 14 Oct 2010 09:40
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#2: Not so easy, writable parameters need to have the proper editor, which assure to have correct data. That is the purpose of the UI panel so it would be redundant.
#3: A 'Select All' and 'Unselect All' option is available when you right click on the panel.
Statistics:Posted by mbastian — 14 Oct 2010 09:00
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Issue #1: When adding a new filter to the queries, one must also click on it to open its settings panel.
Solution: As this is an always repeated action, we could automatically open the filter panel as soon as it is added to the queries.
Issue #2: Parameters are read-only values. This can confuse someone working directly with the tree.
Solution: Writable parameters
Issue #3: Working with several partitions is not easy with the current UI: each partition has to be selected or unselected, so if someone wants to see all the partitions but one, he has to individually select nearly all of them. And he has to manually unselect each one if he wants to see only one after that.
Solution: A button to select or unselect all partitions in one click.
This thread is to discuss on these issues and possible solutions
Statistics:Posted by admin — 13 Oct 2010 22:45
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