Question: emacs org mode html export using jQuery DataTables (WAS: new package for generating interactive HTML reports)
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gravatar for Malcolm Cook
6.6 years ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:
Michael, I forget to pass along the workaround for the one DataTables bug I've found and not yet kicked upstream ## BUG: the sSwfPath above is ignored!!! - The means for overridding the Default (of ## media/swf/copy_csv_xls.swf seems not to work ## http://datatables.net/release- datatables/extras/TableTools/swf_path.html ## WORKAROUNDS: ## 1) create a symlink in the same dir as the org file named ./media to point to /..../js/DataTables/extras/TableTools/media ## 2) BETTER: change the default sSwfPath in ##/..../js/DataTables/extras/TableTools/media/js/TableTools.min.js ## to point to "/.../js/DataTables/extras/TableTools/media/swf/copy_csv_xls.swf" ~Malcolm .-----Original Message----- .From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Cook, Malcolm .Sent: Friday, January 11, 2013 3:55 PM .To: 'Michael Lawrence' .Cc: 'bioconductor at r-project.org' .Subject: Re: [BioC] new package for generating interactive HTML reports . .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/useful/place/js/DataTables/media/css/jquery.dataTables.c ss"></script> .#+STYLE: <script type="text/javascript" charset="utf8" .src="/some/useful/place/js/DataTables/media/js/jquery.dataTables.min .js"></script> .#+STYLE: <script type="text/javascript" charset="utf8" .src="/some/useful/place/js/DataTables/extras/TableTools/media/js/Tab leTools.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_c sv_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 at 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 at="" stowers.org<mailto:mec="" at="" 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 at r-project.org<mailto:bioconductor- bounces="" at="" r-project.org=""> [mailto: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<mailto: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<mailto: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<mailto: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<mailto: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/*<http: biocondu="" ctor.org="" packages="" **devel="" bioc="" html="" *=""> . .> >> >> *ReportingTools.html< . .> >> . .> http://www.bioconductor.org/packages/devel/bioc/html/ReportingTo ols.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 at vhir.org<mailto:xavier.depedro at="" vhir.org=""> . .> >> > http://ueb.vhir.org . .> >> > . .> >> > . .> >> > ______________________________**_________________ . .> >> > Bioconductor mailing list . .> >> > Bioconductor at r-project.org<mailto:bioconductor at="" 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 at r-project.org<mailto:bioconductor at="" 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 at gene.com<mailto:huntley.melanie at="" gene.com=""> . .> > . .> > [[alternative HTML version deleted]] . .> > . .> > _______________________________________________ . .> > Bioconductor mailing list . .> > Bioconductor at r-project.org<mailto:bioconductor at="" 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 at gene.com<mailto:huntley.melanie at="" gene.com=""> . . . . [[alternative HTML version deleted]] . . . ._______________________________________________ . .Bioconductor mailing list . .Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> . .https://stat.ethz.ch/mailman/listinfo/bioconductor . .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor . . . [[alternative HTML version deleted]] . ._______________________________________________ .Bioconductor mailing list .Bioconductor at r-project.org .https://stat.ethz.ch/mailman/listinfo/bioconductor .Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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