Michael,
Glad to oblige.
Assuming you already know org-mode/emacs....
* install DataTables from
http://datatables.net/ in
/some/useful/place/js/DataTables
* put this in the 1st line of your .org file: # -*- org-
export-babel-evaluate: nil; org-export-allow-BIND: t -*-
* put another line in your .org file like this: #+SETUPFILE:
"/some/useful/place/org/SETUPFILE.org"
* put the following text in
/some/useful/place/org/SETUPFILE.org :
######################################################################
##########
## Making all org exported tables be, by default,
## sortable/filterable/pagable/...
## NOTE: #+BIND requires, to avoid prompting on each export, that
## org-export-allow-BIND be t, as is indicated to emacs with "-*-
modeline ; org-export-allow-BIND: t -*-"
## Something to do with security ;)
######################################################################
##########
#+BIND: org-export-html-table-tag ""
#+STYLE: <script type="text/javascript" charset="utf8" src="/some/useful/place/js/DataTables/media/js/jquery.js"></script>
#+STYLE: <link rel="stylesheet" type="text/css" href="/some/usef
ul/place/js/DataTables/media/css/jquery.dataTables.css"></script>
#+STYLE: <script type="text/javascript" charset="utf8" src="/some/usef
ul/place/js/DataTables/media/js/jquery.dataTables.min.js"></script>
#+STYLE: <script type="text/javascript" charset="utf8" src="/some/usef
ul/place/js/DataTables/extras/TableTools/media/js/TableTools.min.js"><
/script>
#+STYLE: <script type="text/javascript">$(document).ready(function(){$
('.dataTable').dataTable({"sPaginationType":
"full_numbers","sScrollX": "100%", "bStateSave": true, "bProcessing":
true, "bDeferRender": true, "aaSorting": [] , "sDom":
'ClifrtrpT<"afterTable">', "oTableTools": { "sSwfPath": "/some/useful/
place/js/DataTables/extras/TableTools/media/swf/copy_csv_xls.swf"}});
$("div.afterTable").html('
');});</script>
Your paths may vary. These worked at the time of deployment a few
months ago.
To have DataTable sort on p-values and other scientific notation, put
another line in our SETUPFILE.org: #+STYLE: <script type="text/javascript" src="/some/useful/place/js/myDatatableUtil.js"></script>
...and put the following in that file:
jQuery.fn.dataTableExt.aTypes.unshift(
function ( sData )
{
if (! isNaN(parseFloat(sData))) {
return 'scientific';
}
return null;
}
);
jQuery.extend( jQuery.fn.dataTableExt.oSort, {
"scientific-pre": function ( a ) {
return parseFloat(a);
},
"scientific-asc": function ( a, b ) {
return ((a < b || isNaN(a)) ? -1 : ((a > b || isNaN(b)) ? 1 :
0));
},
"scientific-desc": function ( a, b ) {
return ((a < b || isNaN(a)) ? 1 : ((a > b || isNaN(b)) ? -1 :
0));
}
} );
~Malcolm
From: Michael Lawrence [mailto:lawrence.michael@gene.com]
Sent: Friday, January 11, 2013 3:11 PM
To: Cook, Malcolm
Subject: Re: [BioC] new package for generating interactive HTML
reports
Hi Malcolm,
That sounds really cool. Mind passing me the magic style options? Or a
URL?
Thanks,
Michael
On Fri, Jan 11, 2013 at 12:13 PM, Cook, Malcolm
<mec@stowers.org<mailto:mec@stowers.org>> wrote:
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@r-project.org<mailto:bioconductor- bounces@r-project.org=""> [mailto:bioconductor-
bounces@r-project.org<mailto:bioconductor-bounces@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@r-project.org<mailto:bioconductor@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@mail.nih.gov<mailto:sdavis2@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@gene.com<mailto:lawrence.michael@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@vhir.org<mailto:xavier.depedro@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/*<http: bioconduct="" or.org="" packages="" **devel="" bioc="" html="" *="">
.> >> >> *ReportingTools.html<
.> >>
.>
http://www.bioconductor.org/packages/devel/bioc/html/ReportingTool
s.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<tel:%2b34%20934894007> / Fax +34
934894015<tel:%2b34%20934894015>
.> >> > xavier.depedro@vhir.org<mailto:xavier.depedro@vhir.org>
.> >> >
http://ueb.vhir.org
.> >> >
.> >> >
.> >> > ______________________________**_________________
.> >> > Bioconductor mailing list
.> >> > Bioconductor@r-project.org<mailto:bioconductor@r-project.org>
.> >> >
https://stat.ethz.ch/mailman/**listinfo/bioconductor<
.> >>
https://stat.ethz.ch/mailman/listinfo/bioconductor>
.> >> > Search the archives:
http://news.gmane.org/gmane.**
.> >> > science.biology.informatics.**conductor<
.> >>
http://news.gmane.org/gmane.science.biology.informatics.conductor>
.> >> >
.> >>
.> >> [[alternative HTML version deleted]]
.> >>
.> >> _______________________________________________
.> >> Bioconductor mailing list
.> >> Bioconductor@r-project.org<mailto:bioconductor@r-project.org>
.> >>
https://stat.ethz.ch/mailman/listinfo/bioconductor
.> >> Search the archives:
.> >>
http://news.gmane.org/gmane.science.biology.informatics.conductor
.> >>
.> >
.> >
.> >
.> > --
.> > Melanie Huntley, Ph.D
.> > Bioinformatics and Computational Biology
.> > Genentech, Inc.
.> > huntley.melanie@gene.com<mailto:huntley.melanie@gene.com>
.> >
.> > [[alternative HTML version deleted]]
.> >
.> > _______________________________________________
.> > Bioconductor mailing list
.> > Bioconductor@r-project.org<mailto:bioconductor@r-project.org>
.> >
https://stat.ethz.ch/mailman/listinfo/bioconductor
.> > Search the archives:
.>
http://news.gmane.org/gmane.science.biology.informatics.conductor
.>
.
.
.
.--
.Melanie Huntley, Ph.D
.Bioinformatics and Computational Biology
.Genentech, Inc.
.huntley.melanie@gene.com<mailto:huntley.melanie@gene.com>
.
. [[alternative HTML version deleted]]
.
._______________________________________________
.Bioconductor mailing list
.Bioconductor@r-project.org<mailto:bioconductor@r-project.org>
.https://stat.ethz.ch/mailman/listinfo/bioconductor
.Search the archives:
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