Re: [Jtreeview-users] Question about TreeView and PCA

[Alok S. <al...@ca...>]

Dear Hrishi,

There is currently no PCA-specific view in java treeview. Hopefully,  
this will change at some point in the future, but I unfortunately  
don't have time to add a PCA viewer. I will be adding a plugin  
interface to the next version, this should make it somewhat easier to  
add new views, but the PCA data is really quite different from the  
other ways of clustering, and will still take some work before it is  
ready to go.

I will give you some ideas on what you can do in the meantime. There  
should be an "svu.txt" file and an "svv.txt" file. I will describe  
them separately:

SVU:

To open this file, you must go to file->open Java Treeview, and then  
select the "All Files" option from the file format pulldown.

When the file opens, most likely you will see a black rectangle. This  
is because the values in are normalized to between 0 and 1, and  
typically have values around 1/N, where N is the number of genes in  
the dataset, which just shows up as black in java treeview. To fix  
this, go to "Settings->Pixel Settings..." and set the contrast to 1/ 
N, more or less, and you should be able to see things. The gene names  
should be as expected, and the array names will be replaced with the  
eigen values of the corresponding eigen arrays.


SVV:

This is tricker, since the format of the _svv.txt files does not  
correspond with what JTV expects. You must do the following:

1) open in Excel or other spreadsheet program
2) duplicate the EIGVALUE column. The first two columns in java  
treeview are supposed to be identifiers; doubling this column will  
just make an extra column for each eigen gene. The "names" of the  
eigen genes will be the associated eigenvalues.
3) Save the file as "tab delimitted text".

Now, you should be able to open and view the data in java treeview.

As a quick fix, I could add some detection code to java treeview to  
do these manipulations automatically when it sees a EIGVALUE first  
column, and no GWEIGHT column. Do you think this would be useful?

     Take care,
     Alok

On Aug 31, 2005, at 7:07 AM, Hrishikesh Deshmukh wrote:

> Hi All,
>
> I have used Cluster 3.0 to calculate PCA results but how does one  
> use TreeView to visualize results?!
>
> Thanks,
> Hrishi