[Jtreeview-users] Re: Problems with Treeview

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

Dear Christina,

I will do my best to answer your questions, feel free to ask for 
clarifications.

On Oct 17, 2004, at 7:28 PM, christina curtis wrote:

> Hello Dr. Saldanha,
>
> I have been attempting to use your Treeview program, but have 
> encountered several problems that I hope you might be able to address.
>
> The first, most concerning problem is that the dendrogram mostly 
> appears to have certain lines sticking out from various nodes, but the 
> overall connectedness is difficult to view. It looks as though there 
> may be one long edge connecting many of the children nodes (rather 
> than a step level appearance as one typically sees) however, this one 
> line is so close to the edge of the page that it is difficult to see 
> and remains difficult to see when I export the data.

I am not 100% sure what you are getting at... could you send a 
screenshot? You may be able to increase resolution by dedicating more 
of the screen to the tree (click on the black borders), but most likely 
the clusters all have similar correlation, which causes the steps to 
overlap. This is common with so few samples.

> Is this unusual and is there something I can do to change the 
> appearance?
>
> Secondly, what is the best way to deal with the complete dendrogram 
> once it has been exported. I am interested in viewing roughly 1200 
> genes at once (only two samples) however, this takes up many many 
> pages if one wants to actually be able to read the gene names. Do you 
> recommend simply shrinking the overall size down for presentation 
> purposes and then zooming in on regions of interest?

I do recommend shrinking the size down. This can most easily be done by 
selecting "Settings->Pixel Settings..." and then messing around with 
the Global and Zoom boxes. For starters, I recommend clicking the 
"Fill" boxes in the Global box, but try different numbers to see how it 
all works. When you go to export, select "Export->Save Thumbnail Image" 
and it will use the Global settings.


> Another point of concern is that from the manual it seems to me that 
> there are other plotting options available, namely, the scatterplot. 
> However, when I go to "Analysis" the only options are find, model 
> stats and summary window. The model stats does not seem to do 
> anything. Why is it that these functions do not load? I have tried 
> with both the 1.0.7 and 1.0.8 version.
>

How exactly are you starting Java Treeview? From the command line, you 
need to run the LinkedView application, not the TreeView.
There are actually several slightly different applications in the 
TreeView.jar, and I haven't been careful about which gets used when. 
What you are describing is consistent with running the Treeview instead 
of LinkedView, probably with something like

java -cp TreeView.jar TreeView

Try

java -jar -Xmx500m TreeView.jar

instead, as it should use the correct main class. I am sorry for this 
point of confusion.

	Good Luck!
	Alok