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.

AuthorNils Gehlenborg <>
Date of publication2013-05-15 19:25:56
MaintainerNils Gehlenborg <>

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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.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,

getDoiCreator: Get the DOI creator for 'report'.

getDoiPublisher: Get the DOI publisher for 'report'.

getDoiResolver: Get the DOI resolver URL (e.g. 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.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.


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,

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. 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/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

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