[BioC] Using htmlpage

[john seers (IFR)]

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. 

>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?

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