Nozzle.R1: Nozzle Reports

The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.

Author
Nils Gehlenborg <nils@hms.harvard.edu>
Date of publication
2013-05-15 19:25:56
Maintainer
Nils Gehlenborg <nils@hms.harvard.edu>
License
LGPL-2
Version
1.1-1
URLs

View on CRAN

Man pages

addTo
Add child elements to a parent element.
addToInput
Add elements to the "Input" subsection in the "Methods &...
addToIntroduction
Add elements to the "Introduction" subsection in the...
addToMeta
Add elements to the "Meta" section of a standard report.
addToMethods
Add elements to the "Methds & Data" section of a standard...
addToOverview
Add elements to the "Overview" section of a standard report.
addToReferences
Add elements to the "References" subsection in the "Methods &...
addToResults
Add elements to the "Results" section of a standard report.
addToSummary
Add elements to the "Summary" subsection in the "Overview"...
asCode
Format text as code.
asEmph
Format text with emphasis (usually resulting in text set in...
asFilename
Format text as filename.
asLink
Format text as a hyperlink.
asParameter
Format text as parameter.
asReference
Reference a citation, figure or table element.
asStrong
Format text with strong emphasis (usually resulting in text...
asSummary
Include a result in text. This is a legacy method and...
asValue
Format text as value.
DEFAULT.DOI.RESOLVER
Default DOI resolver URL.
DEFAULT.REPORT.FILENAME
Default filename for reports.
DEFAULT.SIGNIFICANT.ENTITY
Name of entities that are labeled as signficiant.
getContactInformationEmail
Get contact email address for 'report'.
getContactInformationLabel
Get label for contact button for 'report'.
getContactInformationMessage
Get contact email default message for 'report'.
getContactInformationSubject
Get contact email subject line for 'report'.
getCopyrightOwner
Get name of the copyright owner for 'report'.
getCopyrightStatement
Get copyright statement for 'report'. This text is linked to...
getCopyrightUrl
Get copyright URL for 'report', which is linked to the...
getCopyrightYear
Get copyright year 'report'.
getCreatorDate
Get date when 'report' was created.
getCreatorName
Get name and version of the Nozzle package that was used to...
getCustomPrintCss
Get the path or URL of the CSS file to be used to overwrite...
getCustomScreenCss
Get the path or URL of the CSS file to be used to overwrite...
getDoi
Get the DOI (document object identifier, http://www.doi.org)...
getDoiCreator
Get the DOI creator for 'report'.
getDoiPublisher
Get the DOI publisher for 'report'.
getDoiResolver
Get the DOI resolver URL (e.g. http://dx.doi.org) for...
getDoiTitle
Get the DOI title for 'report'.
getDoiVersion
Get the DOI version for 'report'.
getDoiYear
Get the DOI year for 'report'.
getExportedElement
Get an exported element from a report. This can be used to...
getExportedElementIds
Get the IDs of exported elements from 'report'. This is an...
getFigureFile
Get path or URL of image file associated with a figure...
getFigureFileHighRes
Get path or URL of high-resolution of vector-based image file...
getGoogleAnalyticsId
Get Google Analytics tracking ID for 'report'.
getLogo
Get logo file for one of six positions (three at the top,...
getMaintainerAffiliation
Get affiliation of maintainer of 'report'.
getMaintainerEmail
Get email address of maintainer of 'report'.
getMaintainerName
Get name of maintainer of 'report'.
getRendererDate
Get date when 'report' was rendered.
getRendererName
Get name and version of the Nozzle package that was used to...
getReportId
Get the ID (a UUID) of 'report'.
getReportSubtitle
Get the subtitle of 'report'.
getReportTitle
Get the title of 'report'.
getSignificantEntity
Get name of entities that are called out as significant, e.g....
getSignificantResultsCount
Get the total number of significant results in 'report'.
getSoftwareName
Get the name of the software that used Nozzle to generate...
getSoftwareVersion
Get the version of the software that used Nozzle to generate...
getSummary
Get the first element of the "Summary" subsection in the...
getTableFile
Get path or URL of file associatd with table element.
HTML.FRAGMENT
Output type.
HTML.REPORT
Output type.
IMAGE.TYPE.PDF
Image type.
IMAGE.TYPE.RASTER
Image type.
IMAGE.TYPE.SVG
Image type.
isFigure
Test if 'element' is a figure element.
isTable
Test if 'element' is a table element.
LOGO.BOTTOM.CENTER
Logo position.
LOGO.BOTTOM.LEFT
Logo position.
LOGO.BOTTOM.RIGHT
Logo position.
LOGO.TOP.CENTER
Logo position.
LOGO.TOP.LEFT
Logo position.
LOGO.TOP.RIGHT
Logo position.
newCitation
Create a citation element.
newCustomReport
Create a new custom report without pre-defined sections.
newFigure
Create a new list element.
newHtml
Create a new freeform HTML element. THIS MUST BE USED WITH...
newJournalCitation
Create a citation element that represents a document...
newList
Create a new list element.
newParagraph
Create a new paragraph element.
newParameterList
Create a new parameter list element. A parameter list is an...
newReport
Create a new report with pre-defined sections...
newResult
Create a new result element.
newSection
Create a new section element.
newSubSection
Create a new subsection element.
newSubSubSection
Create a new subsubsection element.
newTable
Create new table element.
newWebCitation
Create a citation element that represents a document...
Nozzle.R1-package
Nozzle: a Report Generation Toolkit for Data Analysis...
PROTECTION.GROUP
Group visibility.
PROTECTION.PRIVATE
Private visibility.
PROTECTION.PUBLIC
Public visibility.
PROTECTION.TCGA
Group visibility.
RDATA.REPORT
Output type.
SECTION.CLASS.META
Section class.
SECTION.CLASS.RESULTS
Section class.
setContactInformation
Set contact information for 'report'. This is used to create...
setCopyright
Set copyright messsage for 'report'.
setCustomPrintCss
Set the path or URL of the CSS file to be used to overwrite...
setCustomScreenCss
Set the path or URL of the CSS file to be used to overwrite...
setDoi
Set the DOI (document object identifier, http://www.doi.org)...
setDoiCreator
Set the DOI meta data creator for 'report'.
setDoiPublisher
Set the DOI meta data publisher for 'report'.
setDoiResolver
Set the DOI resolver URL (e.g. http://dx.doi.org) for...
setDoiTitle
Set the DOI meta data title for 'report'.
setDoiVersion
Set the DOI meta data version for 'report'.
setDoiYear
Set the DOI meta data year for 'report'.
setFigureFile
Set path or URL of image file associated with a figure...
setFigureFileHighRes
Set path or URL of high-resolution or vector-based image file...
setGoogleAnalyticsId
Set the Google Analytics tracking ID to be embedded in this...
setLogo
Set a logo file for one of six positions (three at the top,...
setMaintainerAffiliation
Set affiliation of maintainer of 'report'.
setMaintainerEmail
Set email address of maintainer of 'report'.
setMaintainerName
Set name of maintainer of 'report'.
setNextReport
Set the URL and title of the "next" report after 'report'....
setParentReport
Set the URL and title of the "parent" report above 'report'....
setPreviousReport
Set the URL and title of the "previous" report before...
setReportSubtitle
Set the subtitle of 'report'.
setReportTitle
Set the title of 'report'.
setSignificantEntity
Set name of entities that are called out as significant, e.g....
setSoftwareName
Set the name of the software that used Nozzle to generate...
setSoftwareVersion
Set the name of the software that used Nozzle to generate...
setTableFile
Set path or URL of file associatd with table element.
TABLE.SIGNIFICANT.DIGITS
Default number of significant digits to be used to trim...
writeReport
Write 'report' to file.

Files in this package

Nozzle.R1
Nozzle.R1/MD5
Nozzle.R1/R
Nozzle.R1/R/nozzle.R
Nozzle.R1/NEWS
Nozzle.R1/NAMESPACE
Nozzle.R1/man
Nozzle.R1/man/writeReport.Rd
Nozzle.R1/man/TABLE.SIGNIFICANT.DIGITS.Rd
Nozzle.R1/man/setTableFile.Rd
Nozzle.R1/man/setSoftwareVersion.Rd
Nozzle.R1/man/setSoftwareName.Rd
Nozzle.R1/man/setSignificantEntity.Rd
Nozzle.R1/man/setReportTitle.Rd
Nozzle.R1/man/setReportSubtitle.Rd
Nozzle.R1/man/setPreviousReport.Rd
Nozzle.R1/man/setParentReport.Rd
Nozzle.R1/man/setNextReport.Rd
Nozzle.R1/man/setMaintainerName.Rd
Nozzle.R1/man/setMaintainerEmail.Rd
Nozzle.R1/man/setMaintainerAffiliation.Rd
Nozzle.R1/man/setLogo.Rd
Nozzle.R1/man/setGoogleAnalyticsId.Rd
Nozzle.R1/man/setFigureFileHighRes.Rd
Nozzle.R1/man/setFigureFile.Rd
Nozzle.R1/man/setDoiYear.Rd
Nozzle.R1/man/setDoiVersion.Rd
Nozzle.R1/man/setDoiTitle.Rd
Nozzle.R1/man/setDoiResolver.Rd
Nozzle.R1/man/setDoiPublisher.Rd
Nozzle.R1/man/setDoiCreator.Rd
Nozzle.R1/man/setDoi.Rd
Nozzle.R1/man/setCustomScreenCss.Rd
Nozzle.R1/man/setCustomPrintCss.Rd
Nozzle.R1/man/setCopyright.Rd
Nozzle.R1/man/setContactInformation.Rd
Nozzle.R1/man/SECTION.CLASS.RESULTS.Rd
Nozzle.R1/man/SECTION.CLASS.META.Rd
Nozzle.R1/man/RDATA.REPORT.Rd
Nozzle.R1/man/PROTECTION.TCGA.Rd
Nozzle.R1/man/PROTECTION.PUBLIC.Rd
Nozzle.R1/man/PROTECTION.PRIVATE.Rd
Nozzle.R1/man/PROTECTION.GROUP.Rd
Nozzle.R1/man/Nozzle.R1-package.Rd
Nozzle.R1/man/newWebCitation.Rd
Nozzle.R1/man/newTable.Rd
Nozzle.R1/man/newSubSubSection.Rd
Nozzle.R1/man/newSubSection.Rd
Nozzle.R1/man/newSection.Rd
Nozzle.R1/man/newResult.Rd
Nozzle.R1/man/newReport.Rd
Nozzle.R1/man/newParameterList.Rd
Nozzle.R1/man/newParagraph.Rd
Nozzle.R1/man/newList.Rd
Nozzle.R1/man/newJournalCitation.Rd
Nozzle.R1/man/newHtml.Rd
Nozzle.R1/man/newFigure.Rd
Nozzle.R1/man/newCustomReport.Rd
Nozzle.R1/man/newCitation.Rd
Nozzle.R1/man/LOGO.TOP.RIGHT.Rd
Nozzle.R1/man/LOGO.TOP.LEFT.Rd
Nozzle.R1/man/LOGO.TOP.CENTER.Rd
Nozzle.R1/man/LOGO.BOTTOM.RIGHT.Rd
Nozzle.R1/man/LOGO.BOTTOM.LEFT.Rd
Nozzle.R1/man/LOGO.BOTTOM.CENTER.Rd
Nozzle.R1/man/isTable.Rd
Nozzle.R1/man/isFigure.Rd
Nozzle.R1/man/IMAGE.TYPE.SVG.Rd
Nozzle.R1/man/IMAGE.TYPE.RASTER.Rd
Nozzle.R1/man/IMAGE.TYPE.PDF.Rd
Nozzle.R1/man/HTML.REPORT.Rd
Nozzle.R1/man/HTML.FRAGMENT.Rd
Nozzle.R1/man/getTableFile.Rd
Nozzle.R1/man/getSummary.Rd
Nozzle.R1/man/getSoftwareVersion.Rd
Nozzle.R1/man/getSoftwareName.Rd
Nozzle.R1/man/getSignificantResultsCount.Rd
Nozzle.R1/man/getSignificantEntity.Rd
Nozzle.R1/man/getReportTitle.Rd
Nozzle.R1/man/getReportSubtitle.Rd
Nozzle.R1/man/getReportId.Rd
Nozzle.R1/man/getRendererName.Rd
Nozzle.R1/man/getRendererDate.Rd
Nozzle.R1/man/getMaintainerName.Rd
Nozzle.R1/man/getMaintainerEmail.Rd
Nozzle.R1/man/getMaintainerAffiliation.Rd
Nozzle.R1/man/getLogo.Rd
Nozzle.R1/man/getGoogleAnalyticsId.Rd
Nozzle.R1/man/getFigureFileHighRes.Rd
Nozzle.R1/man/getFigureFile.Rd
Nozzle.R1/man/getExportedElementIds.Rd
Nozzle.R1/man/getExportedElement.Rd
Nozzle.R1/man/getDoiYear.Rd
Nozzle.R1/man/getDoiVersion.Rd
Nozzle.R1/man/getDoiTitle.Rd
Nozzle.R1/man/getDoiResolver.Rd
Nozzle.R1/man/getDoiPublisher.Rd
Nozzle.R1/man/getDoiCreator.Rd
Nozzle.R1/man/getDoi.Rd
Nozzle.R1/man/getCustomScreenCss.Rd
Nozzle.R1/man/getCustomPrintCss.Rd
Nozzle.R1/man/getCreatorName.Rd
Nozzle.R1/man/getCreatorDate.Rd
Nozzle.R1/man/getCopyrightYear.Rd
Nozzle.R1/man/getCopyrightUrl.Rd
Nozzle.R1/man/getCopyrightStatement.Rd
Nozzle.R1/man/getCopyrightOwner.Rd
Nozzle.R1/man/getContactInformationSubject.Rd
Nozzle.R1/man/getContactInformationMessage.Rd
Nozzle.R1/man/getContactInformationLabel.Rd
Nozzle.R1/man/getContactInformationEmail.Rd
Nozzle.R1/man/DEFAULT.SIGNIFICANT.ENTITY.Rd
Nozzle.R1/man/DEFAULT.REPORT.FILENAME.Rd
Nozzle.R1/man/DEFAULT.DOI.RESOLVER.Rd
Nozzle.R1/man/asValue.Rd
Nozzle.R1/man/asSummary.Rd
Nozzle.R1/man/asStrong.Rd
Nozzle.R1/man/asReference.Rd
Nozzle.R1/man/asParameter.Rd
Nozzle.R1/man/asLink.Rd
Nozzle.R1/man/asFilename.Rd
Nozzle.R1/man/asEmph.Rd
Nozzle.R1/man/asCode.Rd
Nozzle.R1/man/addToSummary.Rd
Nozzle.R1/man/addToResults.Rd
Nozzle.R1/man/addToReferences.Rd
Nozzle.R1/man/addToOverview.Rd
Nozzle.R1/man/addToMethods.Rd
Nozzle.R1/man/addToMeta.Rd
Nozzle.R1/man/addToIntroduction.Rd
Nozzle.R1/man/addToInput.Rd
Nozzle.R1/man/addTo.Rd
Nozzle.R1/inst
Nozzle.R1/inst/js
Nozzle.R1/inst/js/nozzle.min.js
Nozzle.R1/inst/js/nozzle.js
Nozzle.R1/inst/js/jquery.tablesorter.min.js
Nozzle.R1/inst/js/jquery.tablesorter.js
Nozzle.R1/inst/js/jquery-1.5.1.min.js
Nozzle.R1/inst/js/google-analytics.js
Nozzle.R1/inst/css
Nozzle.R1/inst/css/nozzle_with_print.css
Nozzle.R1/inst/css/nozzle.print.min.css
Nozzle.R1/inst/css/nozzle.print.css
Nozzle.R1/inst/css/nozzle.min.css
Nozzle.R1/inst/css/nozzle.css
Nozzle.R1/DESCRIPTION