[BioC] new package for generating interactive HTML reports

Fri Jan 11 19:53:18 CET 2013

On 01/11/2013 10:37 AM, Melanie Huntley wrote:
> Hi Sean,
>
> There certainly seem to be more available options to speed things up if we
> require the hard work to be done server side - we were considering this in
> the initial phases of the package devel.
>
> Our thinking was to keep things as user friendly as possible to start (ie.
> keep things client side) - but the trade-off has been a decrease in
> responsiveness for very large datasets. Perhaps we should revisit the
> server option again for the next release if we don't find a client side
> solution.

really just shooting from the hip here, but the R package 'shiny' seems to be a 
very nice way to deploy R client / server apps; under the hood I think it's 
using the R 'websockets' library as a modern way to communicate.

Martin

>
> Thanks,
> Melanie
>
> On Fri, Jan 11, 2013 at 10:23 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>>
>> Hi, Melanie.
>>
>> The "extra" scroller for datatables allows scrolling of VERY large
>> datasets because only a small portion of the entire dataset is sent to
>> the client at one time.  The server simply responds to requests for
>> data as the dataset scrolls on the client.  The details are here:
>>
>>
>> http://datatables.net/release-datatables/extras/Scroller/server-side_processing.html
>>
>> This would require a server that responds to queries be running while
>> the client is interacting with the data.
>>
>> Sean
>>
>>
>>
>>> On Fri, Jan 11, 2013 at 7:19 AM, Michael Lawrence <
>> lawrence.michael at gene.com
>>>> wrote:
>>>
>>>> The package is extensible to the point that you could simply create a
>> new
>>>> type of report that is output as some wiki language, so it wouldn't be
>>>> necessary to fork or modify ReportingTools. If there are internal
>> utilities
>>>> for generating data tables that might be usefully shared, they could be
>>>> exposed, or at least factored out for ":::" access.
>>>>
>>>> Michael
>>>>
>>>>
>>>> On Fri, Jan 11, 2013 at 1:02 AM, Xavier de Pedro <
>> xavier.depedro at vhir.org
>>>>> wrote:
>>>>
>>>>> Dear Josh & co.:
>>>>>
>>>>> Thanks for producing such a package, it looks promising indeed!
>>>>>
>>>>> I see that it uses jquery data tables, and the live filtering of the
>> data
>>>>> is very fast (nice!).
>>>>> I have a few quick questions, after a quick review of your vignette
>> and
>>>>> examples:
>>>>>
>>>>> Have you experienced any issues when the data set contained in the
>>>> browser
>>>>> is very large (regardless that you set the browser to display just 10
>>>>> records at a time; I understand that the whole data set is loaded in
>> the
>>>>> browser)?
>>>>>
>>>>> And in my relaxed todo list (without hurries) I had the idea to
>> create a
>>>>> similar package to produce wiki syntax for tables from R data frames,
>> and
>>>>> to display png (or svg) images within pages to be displayed through
>> wiki
>>>>> engines (with it's appropriated syntax for the wiki engine of
>> interest).
>>>> A
>>>>> few years ago I had to do that and I produced some custom function 'ad
>>>> hoc'
>>>>> without releasing it (yet) in any R package. In our example, we run r
>>>>> scripts through Tiki (wiki) pages, through PluginR, but the output is
>>>>> either bare text (so far) or images (png or svg), and any
>> modification is
>>>>> handled by R commands by hand. And a function to produce the "Fancy
>>>> Tables"
>>>>> that Tiki can produce with "JQuery Sortable Tables" is needed (
>>>>> http://doc.tiki.org/**PluginFancyTable<
>>>> http://doc.tiki.org/PluginFancyTable>). I foresee that maybe the
>>>> datatable jquery plugin could be even better
>>>>> for that, since it contains pagination and live filtering, which can
>> be
>>>>> very very handy!.
>>>>>
>>>>> And maybe you are open to receive improvements/extensions to your
>> package
>>>>> to support other ways to produce the tables required for better
>>>> integration
>>>>> for wiki engines such as Tiki? Or should I fork from your package?
>>>>>
>>>>> Thanks in advanced, and congratulations for the generic package that
>> you
>>>>> created.
>>>>>
>>>>> Xavier
>>>>>
>>>>>
>>>>> On 11/01/13 00:49, Josh Kaminker wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> We present a new R package,
>>>>>> ReportingTools<http://www.**
>>>> bioconductor.org/packages/**devel/bioc/html/*
>>>>>> *ReportingTools.html<
>>>>
>> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTools.html>
>>>>>>> ,
>>>>>> for transforming the output of various Bioconductor packages into
>>>>>> interactive web pages.  We have found this package very useful in our
>>>>>> collaborations with both bench and other computational scientists.
>>>>>>   Examples
>>>>>> and instructions for generating output using this package can be
>> found
>>>>>> here: http://research-pub.gene.com/**ReportingTools/<
>>>> http://research-pub.gene.com/ReportingTools/>
>>>>>>
>>>>>> With just three lines of user code, rich HTML documents can be
>> generated
>>>>>> from the result objects produced by several standard Bioconductor
>>>> packages
>>>>>> including edgeR, limma, GOstats, and GSEAlm.  By default,
>> ReportingTools
>>>>>> reports include hyperlinks to relevant external databases and are
>> highly
>>>>>> interactive through the use of filtering and sorting options
>> provided by
>>>>>> open source javascript libraries.  Supporting javascript and css
>>>> libraries
>>>>>> are included with all reports, allowing them to be examined on a
>> local
>>>>>> computer without a network connection.  Additionally, in-line
>> graphics
>>>>>> have
>>>>>> been developed to accompany statistical results to allow convenient
>>>> visual
>>>>>> inspection of underlying raw data.  ReportingTools output is highly
>>>>>> customizable and this package can be used equally well to share
>> results
>>>>>> from automated pipeline processes or individual customized analyses.
>>>>>>
>>>>>> We are very interested in receiving your feedback including feature
>>>>>> requests for this package.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Josh Kaminker
>>>>>> Melanie Huntley
>>>>>> Jason Hackney
>>>>>> Jessica Larson
>>>>>> Christina Chaivorapol
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Xavier de Pedro Puente, Ph.D.
>>>>> Statistics and Bioinformatics Unit (UEB)
>>>>> High Technology Unit (UAT)
>>>>> Vall d'Hebron Research Institute (VHIR). Mediterranean Building
>>>>> Passeig de la Vall d'Hebron, 119-129
>>>>> 08035 Barcelona. Catalonia. Spain
>>>>>   Ph. +34 934894007 / Fax +34 934894015
>>>>> xavier.depedro at vhir.org
>>>>> http://ueb.vhir.org
>>>>>
>>>>>
>>>>> ______________________________**_________________
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>>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> Melanie Huntley, Ph.D
>>> Bioinformatics and Computational Biology
>>> Genentech, Inc.
>>> huntley.melanie at gene.com
>>>
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