[BioC] new package for generating interactive HTML reports

Fri Jan 11 19:23:24 CET 2013

On Fri, Jan 11, 2013 at 11:07 AM, Melanie Huntley
<huntley.melanie at gene.com> wrote:
> Hi Xavier,
>
> Thanks for your comments and suggestions!
>
> In response to your question about issues when the data in the browser is
> very large - yes, we have observed sluggish behavior when, for example, you
> have a table with 20,000+ rows and many columns, including graphics. And in
> fact, the Chrome browser seems to give us the most trouble in those cases.
>
> We'd love to hear about ways to improve this behavior, if anyone has ideas.

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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