Expression correlation app using excel correlation data

[Patrick Gladding]

I need help with building a network from a excel correlation table (attached file). This can apparently be imported using the Expression Correlation plugin, however the data needs to be annotated for Cytoscape to understand what is considered a Node and Edge. Could someone please explain the steps after importing the data to generate a network diagram?

thanks

[Scooter Morris]

Hi Patrick,
   You may want to see if the aMatReader will work for you.  You may need to fill out the upper diagonal of your matrix first, though.

-- scooter

[Patrick Gladding]

Hi Scooter

This worked in terms of importing a file and creating a network, however it just drew a network where all the nodes were connected to the other nodes with no weightings. The numbers in the columns are correlations between the different variables, and shows the strength of a connection, or edge. The column headers and the first column are the nodes and contain the same variables.

Is there some way to translate the numbers into weightings like line thickness or proximity between nodes.

thanks

Patrick

--
You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/oS2doBxU7OA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Patrick Gladding]

Ideally there would be a cutoff where only connections above >0.7 or below <0.7 would be kept and all the others would be blank.

Patrick

[Scooter Morris]

On 02/04/2016 02:25 PM, Patrick Gladding wrote:

Hi Scooter

This worked in terms of importing a file and creating a network, however it just drew a network where all the nodes were connected to the other nodes with no weightings. The numbers in the columns are correlations between the different variables, and shows the strength of a connection, or edge. The column headers and the first column are the nodes and contain the same variables.

There should be an edge column called "weight".  That reflects the value form the table.  Having a cutoff value is a good idea.

-- scooter

Is there some way to translate the numbers into weightings like line thickness or proximity between nodes.

thanks

Patrick

On Fri, Feb 5, 2016 at 3:55 AM, Scooter Morris <sco...@cgl.ucsf.edu> wrote:

Hi Patrick,
   You may want to see if the aMatReader will work for you.  You may need to fill out the upper diagonal of your matrix first, though.

-- scooter

On Tuesday, February 2, 2016 at 6:33:08 PM UTC-8, Patrick Gladding wrote:

I need help with building a network from a excel correlation table (attached file). This can apparently be imported using the Expression Correlation plugin, however the data needs to be annotated for Cytoscape to understand what is considered a Node and Edge. Could someone please explain the steps after importing the data to generate a network diagram?

thanks

--
You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/oS2doBxU7OA/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.