[rkward-devel] Introduction, proposing a HC plugin and may be a bug report

[Jose Maria Polo]

Hi Thomas,
Thanks for your answer I will start to play around and I will let you know.

Best
Jose
PS:BTW, I just wanted to confirm that the bug is as you said. Changing 
the name of the object my.data solves the problem.




On 11/25/2010 06:05 AM, Thomas Friedrichsmeier wrote:
> Hi,
>
> welcome to the list, and thanks for your offer to help. Let's see if we can get
> you going:
>
> On Thursday 25 November 2010, Jose Maria Polo wrote:
>> The first one that I would like to propose is hierarchical clustering (HC).
>>
>> A simple HC, basically a front end for hclust (transposing the data (d)
>> and generating a distance matrix (dist) will be necessary first).
>>
>>   >  t.r = t(data)
>>   >  dist.tr = dist(t.r)
>>   >  hc.tr = hclust(dist.tr, method = "average")
>>   >  plot(hc.tr, hang = -1)
>>
>> Another approach could be to call pvclust, which it calculates something
>> similar. However it also gives p values.
>>
>>   >  result<- pvclust(data, method.dist="cor", method.hclust="average",
>>
>> nboot=1000)
>>
>>   >  plot(result)
>>
>> What do you think?
> Frankly, I have no idea which of these approaches is better. Unless pvclust
> (which package is that?) offers significant advantages compared to the approach
> usin hclust, I'd lean towards using hclust. Since that is in the official
> "stats" package, this will allow to use the plugin without installing an add-
> on package. Also it's a very safe bet that the functions in the "stats"
> package will continue to be supported and stable in the long term.
>
>> Anyway, I am not writting to just make a suggestion. I would like to
>> help as much as I can with this, even if I never have program anything.
> Great!
>
>> I already started reading the information about how to generate a plugin.
>> As suggested in your plugin webpage, I guess that the best way will be
>> to start modifying a plugin that has a similar role.
>> Ideally should be a pluggin that allows to compare as many variables as
>> we want (I was thinking to use the boxplot plugin, but I realized that
>> the boxplot plugin use many variables, but all separated).
>> Any idea or suggestions?
> Well, the boxplot plugin may not be the easiest one to start with, as it's a
> comparatively complex one. Perhaps barplot or dotchart are easier to handle
> for the start.
>
> In order to support multiple variables, you probably want to generate R code
> like this, as a very first step:
>      data<- data.frame (var_a, var_b, var_c, ...)
> This is to collect all selected variables into a single data.frame.
> Achieving this is not all that hard. First make sure, the<varslot>  in your
> .xml-file has the attribute multi="true", to allow selection of serveral
> variables. Then, in the .js-file, use:
>      var xvarsstring = getValue ("x").split ("\n").join (", ");
>      echo ('data<- data.frame (' + xvarstring + ')\n');
>
>> 2) I am not sure if I should report this here, but I think that I found
>> a bug, when I try to use basic statistic the "submit" botton does not
>> turn on.
> Thanks. This has been reported before, but I could never reproduce this. Now I
> found out it happens when you have an object called "my.data" in the
> workspace. Fixed in our SVN repository.
>
> Regards
> Thomas
>
>
> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App&  Earn a Chance To Win $500!
> Tap into the largest installed PC base&  get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
>
>
> _______________________________________________
> RKWard-devel mailing list
> RKWard-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rkward-devel

-- 
Jose Maria Polo, Ph.D.

Massachusetts General Hospital Center for Regenerative Medicine
Harvard Stem Cell Institute

185 Cambridge Street CPZN 4200
Boston MA 02114
617-643-5941 (tel)
617-643-3170 (fax)
polo.josemaria at mgh.harvard.edu
josemariapolo at gmail.com

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.kde.org/pipermail/rkward-devel/attachments/20101126/1c5e549c/attachment.html>