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 <nils@hms.harvard.edu>
Date of publication2013-05-15 19:25:56
MaintainerNils Gehlenborg <nils@hms.harvard.edu>
LicenseLGPL-2
Version1.1-1
http://github.com/parklab/nozzle, http://gdac.broadinstitute.org/nozzle

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.

Functions

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

Files

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

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Please suggest features or report bugs with the GitHub issue tracker.

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