Fwd: [Cytoscape-discuss] Loading the Data before rendering the graph
Barry Demchak
Barry Demchak -- from my mobile phone
From: <tbh...@uic.edu>
Date: Jul 17, 2016 9:12 PM
Subject: [Cytoscape-discuss] Loading the Data before rendering the graph
To: "cytoscape-discuss" <cytoscap...@googlegroups.com>
Cc:
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Alexander Pico
A couple responses... First, 1000 nodes and 2000 edges is still considered a small network in Cytoscape. So, you should have no problem loading the entire thing in Cytoscape and then stepping through it suing filters, selection, first neighbors, etc. Second, Cytoscape provides generic means to access many databases, so there isn't a single solution that supports incremental loading of networks as you describe. We leave it to each database provider and app developer to implement the right solution for their data type and major use cases. So, for example, you can start with a node and expand using PSICQUIC or the AgilentLiteratureSearch tools. If you want to incrementally access your own private data, you can do this using Neo4j and the CyNeo4j app: http://apps.cytoscape.org/apps/cyneo4j
- Alex
On Sunday, July 17, 2016 at 9:14:04 PM UTC-7, Barry Demchak wrote:
Barry Demchak -- from my mobile phone
---------- Forwarded message ----------
From: <tbh...@uic.edu>
Date: Jul 17, 2016 9:12 PM
Subject: [Cytoscape-discuss] Loading the Data before rendering the graph
To: "cytoscape-discuss" <cytoscape-discuss@googlegroups.com>
Cc:I have big amount of graph data (over 1000 nodes, over 2000 edges). and I want an interactive graph exploration. I want to start with graph with one single root node and user will be able to click on it and explore all it's children nodes and this process continues to form a braking sets nodes after clicking on them to form branches. For this I want the data to be already loaded to the cy instance but how do I take the data that is only required based on the user's request? I want to add the nodes and it's data dynamically. Please help me out.--
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Barry Demchak
Hi, tbhara –
In addition to Alex’ comments, there is a methodology for doing what you’re describing, though it’s a little laborious.
Start with the *entire* network loaded. Then select the single node you’re interested in and select first neighbors.
Invert the selection so that the unwanted nodes are selected. Hide the unwanted nodes.
The result will be a network with the nodes you’re interested in, less the node you’re not.
Explore all you want.
When it comes time to expand the network again, select all of the nodes you’re interested in. Unhide all of the hidden nodes, and select first neighbors again. This will expand the selection to more nodes of interest.
Repeat the selection inversion, node hiding, and exploration process from above.
Not really slick, but generally effective.
Note that when you want to save away a set of nodes, you can select them and then create a separate network from the selection.
Is this what you were looking for??
From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Alexander Pico
Sent: Thursday, July 21, 2016 10:17 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] Re: [Cytoscape-discuss] Loading the Data before rendering the graph
Hi tbhara,
A couple responses... First, 1000 nodes and 2000 edges is still considered a small network in Cytoscape. So, you should have no problem loading the entire thing in Cytoscape and then stepping through it suing filters, selection, first neighbors, etc. Second, Cytoscape provides generic means to access many databases, so there isn't a single solution that supports incremental loading of networks as you describe. We leave it to each database provider and app developer to implement the right solution for their data type and major use cases. So, for example, you can start with a node and expand using PSICQUIC or the AgilentLiteratureSearch tools. If you want to incrementally access your own private data, you can do this using Neo4j and the CyNeo4j app: http://apps.cytoscape.org/apps/cyneo4j
- Alex
On Sunday, July 17, 2016 at 9:14:04 PM UTC-7, Barry Demchak wrote:
Barry Demchak -- from my mobile phone
---------- Forwarded message ----------
From: <tbh...@uic.edu>
Date: Jul 17, 2016 9:12 PM
Subject: [Cytoscape-discuss] Loading the Data before rendering the graph
To: "cytoscape-discuss" <cytoscap...@googlegroups.com>
Cc:
I have big amount of graph data (over 1000 nodes, over 2000 edges). and I want an interactive graph exploration. I want to start with graph with one single root node and user will be able to click on it and explore all it's children nodes and this process continues to form a braking sets nodes after clicking on them to form branches. For this I want the data to be already loaded to the cy instance but how do I take the data that is only required based on the user's request? I want to add the nodes and it's data dynamically. Please help me out.
--
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