[BioC] Using htmlpage

[James W. MacDonald]

Hi John,

john seers (IFR) wrote:
> Hi Jim
> 
> Thanks for the reply.
> 
>> Easily is in the eye of the beholder.
> 
> Easily is in the eye of the user. It could be easier. 

True. However, nothing comes free. The cost of having a namespace is 
that it is not simple to add functionality. The benefit is the 
minimization of function masking by other packages and/or things in the 
workspace.

The other side of the coin is the poor soul in a world without 
namespaces who wonders why htmlpage() doesn't work, unaware that the 
object getCells in his workspace is clobbering the getCells() function 
that he knows nothing about.

> 
>> you will need to add the functions to the source package and then 
>> build/install.
> 
> I thought that might be the answer. I do not really want to do that
> because I do not build R from source. It would also create a maintenance
> problem.  
> 
>> What repository are you trying to add?
> 
> I was building links to www.ensembl.org. 
> 
> ########################################################################
> ###################
> 
> I notice that you are one of the authors Jim, so can I add a further
> question/suggested enhancement.
> 
> One of the links that I am building for www.ensembl.org needs more than
> the id to build the query. So I need the helper function to use the id
> plus further information from one of the other columns. Is there a
> recognised way to do this? That is pass the columns/lists through to
> getCells/getQueryLink/helper function so it can build the link from
> multiple values?

I could probably add the functionality for you, but you will have to be 
less mysterious about what you want.

I can divine that you want something like

getQuery4ENS(ids, species)

so that

getQuery4ENS("ENSG00000064961", "Homo_sapiens")

will build

http://www.ensembl.org/Homo_sapiens/Search/Summary?species=Homo_sapiens;idx=;q=ENSG00000064961

But then again, I could be completely wrong.

Best,

Jim

> 
> Regards
> 
> 
> John  
> 
> 
> 
> 
> 
>  
> ---
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 04 February 2009 15:47
> To: john seers (IFR)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Using htmlpage
> 
> Hi John,
> 
> john seers (IFR) wrote:
>> Hello Bioconductor people
>>
>> I am trying to use htmlpage (from the annotate package) so it can
>> generate html links in addition to the types of links already
> provided. 
>> >From the documentation of htmlpage it says:
>>
>> "Additional repositories can easily be added. See getQueryLink for
> more
>> information."
> 
> Easily is in the eye of the beholder. It is actually quite easy, but you
> 
> will need to add the functions to the source package and then 
> build/install. As you have noted, the namespace prevents you from easily
> 
>   modifying the package by dumping new functions in the workspace.
> 
> What repository are you trying to add? It might be easiest to just add 
> the repository to the package itself, if it is something that others 
> might want to use.
> 
> Best,
> 
> Jim
> 
> 
>> But it does not seem as straightforward as I hoped. Trying to modify
> the
>> scripts hits difficulties with namespaces and local names. Can anyone
>> tell me if there is a simpler way? 
>>
>> I defined my own copy of getQueryLink but htmlpage still called the
>> namespace version. This I could change using:
>>
>> assignInNamespace("getQueryLink", getQueryLink, ns="annotate")
>>
>> But then it did not work because getQueryLink could not see the
> original
>> internal scripts such as getQuery4Affy. So I modified the script again
>> to remove all the repositories I did not need. But I still needed the
>> getQuery4Affy helper script so I had to redefine that and use
>> assignInNamespace again.  
>>
>> This seems too complicated. Have I missed an easier way? Any
>> suggestions? 
>>
>>
>>
>>
>> Regards
>>
>>
>> John
>>
>>
>>
>>
> ########################################################################
>> ################################
>>
>>
>>> sessionInfo()
>> R version 2.8.1 (2008-12-22) 
>> i386-pc-mingw32 
>>
>> locale:
>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>> Kingdom.1252;LC_MONETARY=English_United
>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices datasets  utils
> methods
>> [8] base     
>>
>> other attached packages:
>> [1] annotate_1.20.1     xtable_1.5-4        AnnotationDbi_1.4.2
>> [4] Biobase_2.2.1       RWinEdt_1.8-0      
>>
>> loaded via a namespace (and not attached):
>> [1] DBI_0.2-4     RSQLite_0.7-1
>>
>>
>>
>>
>> ---
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

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