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 | +--------------------------------------------------------------------- ------+

I finally had the chance to work on the tkWidgets a little bit and the following are what I did in reaponse to Rafael's comments: >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. Yes, has been done. >2 - drag select Yes, has been done. >3 - two selection boxes: one showing all with suffix "[cC][eE][lL]" in >the path another with all with suffix "[cC][dD][fF]". I put two boxes in but with one showing the files in a given directory based on predefined prefix or suffix and the other showing the files that are selected. I will put something there to allow users to change the prefix/suffix on the fly so that one box can be used to disply e. g. the [cC][eE][lL] and [cC][dD][fF] files. >4 - areas for writing in information needed. for example, comments, >annotation, names for columns, file to read phenodata from, etc.. Not yet. Jianhua