[BioC] tkctk widgets

[Robert Gentleman]

Below is a request from Rafael regarding some work that Jianhua has
been doing with tcl/tk widgets.
I am hoping that this might be of more general interest to
bioconductor participants (and hence have forwarded it).

The idea is very simple, we are going to develop a handful of widgets
to provide some simple functionality. (I don't believe that menus are
an option, but all sorts of popups are). Initial work will be in tcltk
but if Gtk stabalizes it may well be worth moving over to it (since it
is much richer).

There are some examples there now,
 fileBrowser  -- browse and select files, optional suffix, prefix, and
          arbitrary R functions to control display
 objectBrowser -- soon to allow arbitrary R functions to control
 display (so for example we will show only exprSets).

We are hoping to work, in conjunction with Rafael and Laurent to
develop tools needed to allow a researcher to load up their Affymetrix
data into the affy package and normalize etc using only a point and
click interface.

Some other interesting developments:
  - annotate will (very shortly) have some better tools for grabbing
  things from NCBI (eg pubmed abstracts etc).

Comments and suggestions, such as those below can be sent to the
package developer/maintainer. Especially welcome would be new tools
functions (with documentation, sorry but it has to be that way).

  Regards
    Robert


----- Forwarded message from "Rafael A. Irizarry" <ririzarr@jhsph.edu> -----


Yesterday I tried the tcltk package. I tried the function fileBrowser.
my understadnig is that it only lets you pick one file. a useful function
for affy would let you select various files and return a vector of
filenames. i suggest we start the trial run with this task.

here is some further functionality that would be nice. the list is in
what i suspect is increasing order of dificulty (apologies in advance if
some of these are impossible):

1 -  a click selects a file thats
not selected and deselect a file that is selected. 

2 -  drag select

3 - two selection boxes: one showing all with suffix "[cC][eE][lL]" in
the path another with all with suffix "[cC][dD][fF]". 

4 - areas for writing in information needed. for example, comments,
annotation, names for columns, file to read phenodata from, etc.. 


don't hesitate to ask me to be more specific. 

rafael


On Thu, 7 Mar 2002, Robert Gentleman wrote:

> Hi Laurent, Raphael and Jianhua,
> 
>   I would like to use affy as the test bed for a GUI. We have some
>   tools in place and I think now is the time to try and get enough in
>   place to do some simple things with the affy package. 
> 
>   I would like to get Jianhua to look at what it will take to get
>   widgets for the common tasks.
>   - read in CEL files,
>   - display CEL files as images
>   - normalize, 
>   - compute expression values
> 
>   From Laurent and Raphael we will need some help. I see some code in
>   demos
>   but nothing in the "standard" spot, inst/doc/whaterver.Rnw.
>   It will be important for Jianhua to have a good road map to work
>   from so if you could supply a simple example, working from CEL
>   through to expression (no bells or whistles at this point -- maybe
>   some pointers to where things need to be more adaptable).
> 
>   There is some test data in my account on taniwha that I think can
>   provide a good basis for working from. It is in
>   ~Genetics/Sabain/CLL
>  (Please, this is not for distribution and cannot be copied off of
>   taniwha -- it is an active experiment/analysis).
> 
> 
>    Let me know if you think this is ok (or not).
>     Thanks,
>       Robert
> 
> -- 
> +---------------------------------------------------------------------------+
> | Robert Gentleman                 phone : (617) 632-5250                   |
> | Associate Professor              fax:   (617)  632-2444                   |
> | Department of Biostatistics      office: M1B28
> | Harvard School of Public Health  email: rgentlem@jimmy.dfci.harvard.edu   |
> +---------------------------------------------------------------------------+
> 


----- End forwarded message -----

-- 
+---------------------------------------------------------------------------+
| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B28
| Harvard School of Public Health  email: rgentlem@jimmy.dfci.harvard.edu   |
+---------------------------------------------------------------------------+