[BioC] Using htmlpage

[James W. MacDonald]

Hi John,

john seers (IFR) wrote:

> http://www.ensembl.org/Mus_musculus/Transcript/Exons?t=ENST00000405446
> 
> (N.B. This will not work without a valid transcript). 
> 
> So I need to pull in the transcript id (ENST00000405446) from another
> column but I cannot get to it from the helper function. My clunky
> workaround is to duplicate the transcript column and build the exon
> query on that. So the user finds the exon they are interested in,
> backtracks to transcript column 2 and clicks. I would like them to click
> on the exon id in the exon column. (Transcript column 1 naturally has
> the standard transcript query).

OK, now I understand. You want to build a link using one ID, but 
supplying a different ID to the end user for them to click. This 
functionality still doesn't exist for htmlpage(), as there is no way to 
pass in two sets of IDs, one to build the query and one for the HTML.

And the way htmlpage() is designed, I don't see a simple way to add such 
functionality without making it more of a kludge-fest than it already is.

> 
> But that approach on a specific query misses the point. I was trying not
> to bring it down to specific examples because I think it could be
> completely flexible. But what do I know? I may be completely wrong and
> this is not the philosophy/design of repositories and htmlpage and
> ensembl and I have missed the point of how it should be done. I am not
> in a position to be that prescriptive of how it should be done. Perhaps
> what you have in the code already can do what I want but I just cannot
> see it.

I disagree with this statement. The htmlpage() function isn't designed 
to be completely flexible, nor IMO should it be. It is designed to allow 
relatively inexperienced end users to be able to build html pages of 
their results without having to know loads about html markup and all 
that business.

As it stands it is probably too complicated - I allow people to pass in 
all manner of input and do a lot of probably needless gyrations to 
figure out if what they passed in is OK and then munge it into a 
presentable table. It has been argued more than once that it is too 
complicated (and if I were to simplify, it would almost certainly 
require more rigid inputs and limited outputs).

If you want complete flexibility, then really what you should do is just 
use the xtable package directly. You can create a data.frame containing 
URIs in some of the columns, of whatever form you desire, and then use 
xtable() to build the table and then print it using print(thextable, 
type="html"), which is what is done in htmlpage() (see the last two 
lines of the function).

Best,

Jim



> 
> However I hope that does not sound ungrateful for your efforts because I
> am very grateful. I have not looked at it yet but I am sure you have
> improved the useability of modifying getQueryLink etc which was the main
> difficulty I had. 
> 
>> You will have to run the devel version of R, as the changes are only in
> 
>> the devel version of BioC.
> 
> Oh blow! I guess I cannot resist forever. :)
> 
> 
> Regards and thanks
> 
> 
> John  
> 
> 
> 
> 
> 
> 
> 
>  
> ---
> 
> 
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 13 February 2009 14:36
> To: john seers (IFR)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Using htmlpage
> 
> Hi John,
> 
> john seers (IFR) wrote:
>> Hello Jim
>>
>> Thanks for this. Done impressively quickly.
>>
>>> makes smart use of an environment to hold the getQuery4XX()
> functions,
>> and you 
>>> can add new ones to the environment, thereby bypassing the namespace.
>> It looks like you have found a neat way to do this and to make it a
> lot
>> easier to use. I look forward to giving it a go. I expect I will be
>> curious enough to look at the code and see how it was done.
> 
> As much as I would like to take credit, this is all Martin Morgan.
> 
>>> You can create links to Ensembl, using the repository 'ens'. Since 
>>> AFAICT Ensembl requires a species to be part of the URI, you will
> have 
>>> to pass an additional argument 'species' to htmlpage(). The form of
>> this 
>>> argument is species="Homo_sapiens" for e.g, Human.
>> Ensembl is a good addition. But I am not sure if this particular
>> addition addresses the specific problem I described. But I will have a
>> look and report back to you. That involved an Exon search that needs
> the
>> ensembl transcript id. My workaround for that was to duplicate my
>> transcript column and perform the exon search on that. Perhaps there
> is
>> another way to do it - I will have another go.  
> 
> OK. Given an Ensembl transcript ID (say, ENST00000405446), do you not 
> want to end up here?
> 
> http://www.ensembl.org/Homo_sapiens/Search/Summary?species=Homo_sapiens;
> idx=;q=ENST00000405446
> 
> If not, then where might you want to be?
> 
> As I said in an earlier email, I can only help if you tell me _exactly_ 
> what you want to do. I'm not smart enough to parse what you have said 
> above or in earlier messages. If someone asked me 'What exactly does 
> John Seers want?', I would only be able to say something about you 
> wanting to do something with some data and end up with links to Ensembl.
> 
> And that is seriously not enough to go on.
> 
>> I guess this is, or will be soon, available as a new version of
>> annotate. I will have a look and see if it is there. If not perhaps I
>> will have to give in and follow your recommendation to run from
> source. 
> 
> You will have to run the devel version of R, as the changes are only in 
> the devel version of BioC. The windows binary _would_ have been up there
> 
> today if I hadn't left two uncommented underscores in the help page for 
> htmlpage() (which oddly enough doesn't seem to bother either Linux or 
> Mac OS). So if you want to compile from source, you can start today.
> 
> If you want a windows binary you will have to wait a day or two.
> 
> Best,
> 
> Jim
> 
> 
>> Thanks again. I will give you some feedback on your efforts.
>>
>> Regards
>>
>>
>> John
>>   
>>
>>  
>> ---
>>
>> -----Original Message-----
>> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
>> Sent: 12 February 2009 18:39
>> To: john seers (IFR)
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] Using htmlpage
>>
>> Hi John,
>>
>> Thanks to some help from Martin Morgan (thanks Martin!), the devel 
>> version of annotate now has two additions.
>>
>> 1.) You can create links to Ensembl, using the repository 'ens'. Since
> 
>> AFAICT Ensembl requires a species to be part of the URI, you will have
> 
>> to pass an additional argument 'species' to htmlpage(). The form of
> this
>> argument is species="Homo_sapiens" for e.g, Human. If you forget to
> pass
>> the argument it will bomb out with an error.
>>
>> This should work with ENSG, ENST, or ENSP identifiers, but let me know
> 
>> if you have problems.
>>
>> 2.) You can also now create links for arbitrary websites. There are 
>> three new functions, setRepository(), getRepositories() and 
>> clearRepository() that you can use to set up, look at, and remove 
>> repositories, respectively. This is all thanks to Martin - he makes 
>> smart use of an environment to hold the getQuery4XX() functions, and
> you
>> can add new ones to the environment, thereby bypassing the namespace.
>>
>> The function you add should have similar form to any of the 
>> getQuery4XX() functions. Just write up the function, and use 
>> setRepository() to put it into the environment. There are some
> examples 
>> in the help page for these functions that will hopefully get anyone 
>> interested in this started. Again, let me know if it is not clear, or
> if
>> there are any problems.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> john seers (IFR) wrote:
>>> Hi Jim
>>>
>>>
>>> Searching on ellipsis and pass through I got the following.
>>>
>>> "The second argument to boot(), called 'statistic', can be
>>> any user-written function you want to cook up, with additional
>>> arguments being passed to it through the '...' mechanism after
>>> all of the named arguments. (See: `R-intro `Writing your own
>>> functions `The ellipsis argument for details.)"
>>>
>>> Looking at the boot code shows the user function "statistic" in the
>>> signature and various calls to statistic of the form 
>>>
>>> t0 <- statistic(data, original, rep(1, sum(m)), ...)
>>>
>>>
>>> function (data, statistic, R, sim = "ordinary", stype = "i", 
>>>     strata = rep(1, n), L = NULL, m = 0, weights = NULL, ran.gen =
>>> function(d, 
>>>         p) d, mle = NULL, simple = FALSE, ...) 
>>> {
>>>
>>> This is sort of what I had in mind. (Though I have not found the code
>> to
>>> pass through the "rest" of the variables.). No parsing needed.
>>>
>>>
>>>> However, the ellipsis is designed to pass arbitrary variables to
>>> underlying code.
>>>
>>> I think that is what I am suggesting needs to be done - pass through
>>> arbitrary variables. Perhaps a problem you have is htmlpage calls
>>> getCells which calls getQueryLink which calls the helper function(s).
>>> Not sure if this is any help to you.
>>>
>>> Regards
>>>
>>> John
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>   
>>>  
>>> ---
>>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662