[BioC] new package for generating interactive HTML reports

Cook, Malcolm MEC at stowers.org
Fri Jan 11 21:13:07 CET 2013 

Melanie,

I too have employed the jsQuery dataTable.

I use emacs org mode to generate reports with embedded tables, all of which are made indiscriminately made scrollable/pageable/searchable with the inclusion of a few style directives in the org file.

With the same upsides&downsides you are discussing here.

I recommend it for simple standalone html non-interactive reporting.

In my experience, tens of thousands of rows are easily handled on chrome browser on local area network.

~Malcolm


 .-----Original Message-----
 .From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Melanie Huntley
 .Sent: Friday, January 11, 2013 12:37 PM
 .To: Sean Davis
 .Cc: Josh Kaminker; Michael Lawrence; Melanie Huntley; bioconductor at r-project.org
 .Subject: Re: [BioC] new package for generating interactive HTML reports
 .
 .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.
 .
 .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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 .> >> > Bioconductor at r-project.org
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 .> >> https://stat.ethz.ch/mailman/listinfo/bioconductor>
 .> >> > Search the archives: http://news.gmane.org/gmane.**
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 .> >> http://news.gmane.org/gmane.science.biology.informatics.conductor>
 .> >> >
 .> >>
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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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 .
 .
 .
 .--
 .Melanie Huntley, Ph.D
 .Bioinformatics and Computational Biology
 .Genentech, Inc.
 .huntley.melanie at gene.com
 .
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