ClusterMaker2 Issue--Unable to select Attributes by which to cluster

[Daniel M.]

I've been trying to use ClusterMaker2 and I've run into a pretty big issue.  
When I try to cluster by attribute, make a heatmap or do anything that involves using attributes of nodes, ClusterMaker2 does not give me any options of what attributes I can use.  I have a detailed node table with multiple columns of multiple data types (strings, booleans, integers etc.).  
However, when I try to do something that involves using attributes of nodes--say make a heatmap--where there should be a list of the attributes I have in my node table there is instead an empty whitebox with the word 'None' in it.  
Why is this happening?  How can I cluster by node attributes?  How do I fix this problem? 
Thanks for the help!

[Scooter Morris]

Hi Daniel,
    Can you send me your session file so I can take a look at it?

-- scooter

--
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.
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.

[Daniel M.]

Hi--sorry for the delay.  I can't send you the session file as the data is private.  
Could I use fake data and try to replicate the issue and send you that file?

On Friday, October 14, 2016 at 3:06:09 PM UTC-4, Scooter Morris wrote:

Hi Daniel,
    Can you send me your session file so I can take a look at it?

-- scooter

On 10/14/2016 11:21 AM, Daniel M. wrote:

I've been trying to use ClusterMaker2 and I've run into a pretty big issue.  
When I try to cluster by attribute, make a heatmap or do anything that involves using attributes of nodes, ClusterMaker2 does not give me any options of what attributes I can use.  I have a detailed node table with multiple columns of multiple data types (strings, booleans, integers etc.).  
However, when I try to do something that involves using attributes of nodes--say make a heatmap--where there should be a list of the attributes I have in my node table there is instead an empty whitebox with the word 'None' in it.  
Why is this happening?  How can I cluster by node attributes?  How do I fix this problem? 
Thanks for the help!

--
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-helpdesk+unsub...@googlegroups.com.

[Scooter Morris]

Hi Daniel,
    Absolutely.  That would be great.

-- scooter

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

[Daniel M.]

Hi Scooter--I've figured out the issue.  
Thank you very much for your responses, I really appreciate it!

[Dana Sherill-Rofe]

Hello, I've been having the same problem.. 

My network includes node attributes but the clustermaker2 doesn't allow me to choose them for clustering. 

Thanks! 

Dana

בתאריך יום שישי, 14 באוקטובר 2016 בשעה 22:06:09 UTC+3, מאת Scooter Morris:

Hi Daniel,
    Can you send me your session file so I can take a look at it?

-- scooter

On 10/14/2016 11:21 AM, Daniel M. wrote:

I've been trying to use ClusterMaker2 and I've run into a pretty big issue.  
When I try to cluster by attribute, make a heatmap or do anything that involves using attributes of nodes, ClusterMaker2 does not give me any options of what attributes I can use.  I have a detailed node table with multiple columns of multiple data types (strings, booleans, integers etc.).  
However, when I try to do something that involves using attributes of nodes--say make a heatmap--where there should be a list of the attributes I have in my node table there is instead an empty whitebox with the word 'None' in it.  
Why is this happening?  How can I cluster by node attributes?  How do I fix this problem? 
Thanks for the help!

--
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-helpdesk+unsub...@googlegroups.com.

[Scooter Morris]

Hi Dana,
   Not sure what's going on.  Can you send me a small session file the exhibits the symptoms?

-- scooter

[Dana Sherill-Rofe]

Hi, thanks for your quick answer! I'm attaching the session along with the excel file, I've changed the data from the original file but the structure remains the same. 

Thank your very much for your help,

Dana 

--

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/uyNy_nkVcdU/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.
To post to this group, send email to cytoscape-helpdesk@googlegroups.com.

Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

Dana Sherill-Rofe, PhD

Department of Development Biology and Cancer Research, Faculty of Medicine, 
The Hebrew University of Jerusalem, Ein Kerem.

Danas...@gmail.com

[Scooter Morris]

Hi Dana,
    There are no numerical attributes to use for any of the clustering algorithms in clusterMaker2 in your session, which is why you are getting only "--None--" in the list of Node attributes.  In order to perform any of the attribute clustering techniques you need a set of columns that contain numeric values that can be used to calculate a distance matrix.  Maybe you can explain what you are trying to achieve through "clustering".

-- scooter

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.
To post to this group, send email to cytoscape...@googlegroups.com.

[Dana Sherill-Rofe]

Hi,

I probably used the wrong terms.. I was looking for a way to cluster nodes according to their attributes, so that the network will be ordered to minimize space between nodes with the same attributes while minimize energy. I guess clustermaker is'nt the tool I was looking for. Do you have an idea how I can do that?

Thanks 

Dana 

בתאריך 24 במרץ 2017 20:01,‏ "Scooter Morris" <sco...@cgl.ucsf.edu> כתב:

Hi Dana,
    There are no numerical attributes to use for any of the clustering algorithms in clusterMaker2 in your session, which is why you are getting only "--None--" in the list of Node attributes.  In order to perform any of the attribute clustering techniques you need a set of columns that contain numeric values that can be used to calculate a distance matrix.  Maybe you can explain what you are trying to achieve through "clustering".

-- scooter

On 03/24/2017 12:35 AM, Dana Sherill-Rofe wrote:

Hi, thanks for your quick answer! I'm attaching the session along with the excel file, I've changed the data from the original file but the structure remains the same. 

Thank your very much for your help,

Dana 

2017-03-23 16:10 GMT+02:00 Scooter Morris <sco...@cgl.ucsf.edu>:

Hi Dana,
   Not sure what's going on.  Can you send me a small session file the exhibits the symptoms?

-- scooter

On Friday, October 14, 2016 at 11:21:35 AM UTC-7, Daniel M. wrote:

I've been trying to use ClusterMaker2 and I've run into a pretty big issue.  
When I try to cluster by attribute, make a heatmap or do anything that involves using attributes of nodes, ClusterMaker2 does not give me any options of what attributes I can use.  I have a detailed node table with multiple columns of multiple data types (strings, booleans, integers etc.).  
However, when I try to do something that involves using attributes of nodes--say make a heatmap--where there should be a list of the attributes I have in my node table there is instead an empty whitebox with the word 'None' in it.  
Why is this happening?  How can I cluster by node attributes?  How do I fix this problem? 
Thanks for the help!

--

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/uyNy_nkVcdU/unsubscribe.

To unsubscribe from this group and all its topics, send an email to cytoscape-helpdesk+unsubscribe@googlegroups.com.

To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--

Dana Sherill-Rofe, PhD

Department of Development Biology and Cancer Research, Faculty of Medicine, 
The Hebrew University of Jerusalem, Ein Kerem.

Danas...@gmail.com

--

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-helpdesk+unsub...@googlegroups.com.

To post to this group, send email to cytoscape-helpdesk@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Scooter Morris]

On 03/25/2017 03:02 AM, Dana Sherill-Rofe wrote:

Hi,

I probably used the wrong terms.. I was looking for a way to cluster nodes according to their attributes, so that the network will be ordered to minimize space between nodes with the same attributes while minimize energy. I guess clustermaker is'nt the tool I was looking for. Do you have an idea how I can do that?

Thanks 

Dana 

Hi Dana,
    Right, clusterMaker2 isn't the right tool.  I would suggest looking at the setsApp.  You would define each set based on the attribute.  The setsApp provides it's own layout that you can use to do a force-directed layout that uses sets membership as a "force" to pull sets together.

-- scooter

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.