files input and clustering

[lcollia]

Hi,

I am a new user of Cytoscape. I would like to use it to cluster data.
For example I have this kind of data in a CSV file:

ID property1 property2
s1 1.5 2
s2 2.5 0.5
s3 2 0
s4 3 4

I was thinking that it is possible to cluster these data with the
ClusterMaker plugin but I don't find how to import correctly these
data and how to use these data with ClusterMaker.

Is-it possible? If yes how?

Thanks for your help,

Lionel

[Scooter Morris]

Hi Lionel,
Sure, depending on how you are trying to cluster the data.
Basically you want to import that file as a "network", then import the
attributes (it's a two-pass import). First, import is using the
"File->Import->Network from Table". Select your file. Click on "Show
Text File Import Options" and then select "Transfer first line as
attribute names" read the header. Tthen select the column number of
your ID column as "Source Interaction". Don't select anything else --
just select "Import". That will tell Cytoscape about the nodes to use.
Now we can import all of the attributes (properties) to attach to those
nodes. To do that, use the File->Import->Attributes from Table and
select the same file. As before, click on "Show Text File Import
Options" and transfer the first line as the attribute names. Then just
click "Import". Now you have all of your ID's as nodes, and your
properties are attached to those nodes. You can then cluster the data
using one of the attribute cluster algorithms (Hierarchical, k-means,
etc.) in clusterMaker. Because you don't have any edges, you can't use
a network partition algorithm, obviously, so you won't be able to use
MCL or MCODE. There is a way to create a network from this data based
on attribute correlation in clusterMaker, so you could give that a try also.

Hope this helps!

-- scooter

[lcollia]

Hi Scooter,

Thanks for your help. I can import my data as you explained but I have
a problem when I try to use the "Cluster maker" plugin.

When I click on "create clusters" (for different algorythms) I have
the "error: no attribute list selected". But I don't know how to
select this list.

Thanks,

Lionel

[lcollia]

Hi again,

Finally I change the version of the plugin of ClusterMaker to the 1.8
(and not the 1.9) and now it work.

But ok I can not attribute a cluster number to the node after one
hierarchical clustering or the K-means clustering not seems to finish
(even with 4 nodes and 2 properties...).

Lionel

[Scooter Morris]

Hi Lionel,
You should probably use ClusterMaker 1.10. You'll have to
uninstall 1.8 first, though. Because of a bug in Cytoscape,
clusterMaker 1.10 shows up as clusterMaker 1.1, so you'll see two
clusterMaker 1.1's. Just click on them and the detail will tell you
which one is 1.10 and download that one. However, on to some details...

On 12/23/2011 03:26 AM, lcollia wrote:
> Hi again,
>
> Finally I change the version of the plugin of ClusterMaker to the 1.8
> (and not the 1.9) and now it work.
>
> But ok I can not attribute a cluster number to the node after one
> hierarchical clustering or the K-means clustering not seems to finish
> (even with 4 nodes and 2 properties...).

Well, hierarchical clustering isn't going to really give you a cluster
number that's very meaningful because you'll only get pairs. As for
k-means not finishing, what value did you choose for k?

-- scooter