[BiO BB] plotter and tabular data - visualization

Harry Mangalam harry.mangalam at uci.edu
Wed Feb 14 13:23:29 EST 2007

What you might be thinking of is ggobi (the gtk son of xgobi). 
 It's now integrated well into R and has the interactive brushing 
(highlighting and selecting of points), 3d visualization, 
multi-variate simultaneous visualization, etc.  It is NOT all that 
intuitive to set up for independent use (you have to (or had to) 
re-format your data into XML - ugh), but it works with R data frames 
transparently.  Plus, in R, it has access to all of R's goodies.

If you're going to be doing this more than a one-off, it's a great 
tool and worth the activation energy.

If you want a tool that does just about everything, check out Visit:

and for scripted plotting, it's hard to beat good old gnuplot.  It's 
not particularly interactive, but you can zoom interactively into the 
plot pane for large data sets.  For repetitive plots of large data 
sets, it's fabulous.

Slightly off-topic but only just, you might also want to visit IBM's 
Many Eyes site:

and the similarly tilted http://www.swivel.com

for innovative ways to approach and visualize data.


On Tuesday 13 February 2007 16:19, Ann Loraine wrote:
> Hello all,
> I'm looking for a (kind of) specialized visualization tool, which
> I'm sure must already exist...hopefully one of you can point me in
> the right direction.
> I want something that can read in columns of numbers, where each
> row might be labeled with some value, such as a microarray slide
> id, or something like that.
> Then, I want to plot the columns of numbers against each other (a
> scatter plot), so that I can, by eye, recognize any interesting
> patterns relating one column to another, such as a linear
> relationship, or correlation.
> There are of course lots of programs that can do the plotting part
> relatively easily, but I what I want on top of this is the ability
> to interact with the plot.
> For example, I want the tool to display the original data in a sort
> of Excel-style spreadsheet format, so that I can click on one or
> more rows or cells the spreadsheet and see the corresponding points
> in the plot "light up." Likewise, I want to be able to click on
> points in the plot, and see the corresponding rows get highlighted.
> R has something like this, but it is very clumsy and awkward -- at
> least, it was clumsy and awkard the last time I tried it, which was
> a few years ago. Maybe there's something better now?
> Please let me know if you have used something like this .. or just
> heard about it!
> Yours,
> Ann Loraine

Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c) 
harry.mangalam at uci.edu

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