Nozzle.R1: Nozzle Reports
Version 1.1-1

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.

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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
URL http://github.com/parklab/nozzle http://gdac.broadinstitute.org/nozzle
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Nozzle.R1")

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

DEFAULT.DOI.RESOLVER Man page
DEFAULT.REPORT.FILENAME Man page
DEFAULT.SIGNIFICANT.ENTITY 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
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
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
TABLE.SIGNIFICANT.DIGITS Man page
addResult Source code
addTo Man page Source code
addToElementById Source code
addToInput Man page Source code
addToIntroduction Man page Source code
addToMeta Man page Source code
addToMethods Man page Source code
addToOverview Man page Source code
addToReferences Man page Source code
addToResults Man page Source code
addToSummary Man page Source code
asCode Man page Source code
asEmph Man page Source code
asFilename Man page Source code
asLink Man page Source code
asParameter Man page Source code
asReference Man page Source code
asStrong Man page Source code
asSummary Man page Source code
asValue Man page Source code
comment Source code
concat Source code
countSignificantResults Source code
createIndent Source code
getContactInformationEmail Man page Source code
getContactInformationLabel Man page Source code
getContactInformationMessage Man page Source code
getContactInformationSubject Man page Source code
getCopyrightOwner Man page Source code
getCopyrightStatement Man page Source code
getCopyrightUrl Man page Source code
getCopyrightYear Man page Source code
getCreatorDate Man page Source code
getCreatorName Man page Source code
getCustomPrintCss Man page Source code
getCustomScreenCss Man page Source code
getDoi Man page Source code
getDoiCreator Man page Source code
getDoiPublisher Man page Source code
getDoiResolver Man page Source code
getDoiTitle Man page Source code
getDoiVersion Man page Source code
getDoiYear Man page Source code
getElementById Source code
getExportedElement Man page Source code
getExportedElementIds Man page Source code
getFigureFile Man page Source code
getFigureFileHighRes Man page Source code
getGlobalReportId Source code
getGoogleAnalyticsId Man page Source code
getLogo Man page Source code
getMaintainerAffiliation Man page Source code
getMaintainerEmail Man page Source code
getMaintainerName Man page Source code
getNextCitationNumber Source code
getNextElementId Source code
getNextFigureNumber Source code
getNextResultId Source code
getNextResultNumber Source code
getNextSupplementFigureNumber Source code
getNextSupplementTableNumber Source code
getNextTableNumber Source code
getPackageVersion Source code
getReference Source code
getRendererDate Man page Source code
getRendererName Man page Source code
getReportId Man page Source code
getReportSubTitle Man page Source code
getReportTitle Man page Source code
getSignificantEntity Man page Source code
getSignificantResultsCount Man page Source code
getSoftwareName Man page Source code
getSoftwareVersion Man page Source code
getSummary Man page Source code
getTableFile Man page Source code
hasPredefinedInputSection Source code
hasPredefinedIntroductionSection Source code
hasPredefinedMetaSection Source code
hasPredefinedMethodsSection Source code
hasPredefinedOverviewSection Source code
hasPredefinedReferencesSection Source code
hasPredefinedResultsSection Source code
hasPredefinedSummarySection Source code
isFigure Man page Source code
isTable Man page Source code
log Source code
newCitation Man page Source code
newCustomReport Man page Source code
newElement Source code
newFigure Man page Source code
newGeneralReport Source code
newHtml Man page Source code
newJournalCitation Man page Source code
newList Man page Source code
newParagraph Man page Source code
newParameterList Man page Source code
newReport Man page Source code
newReportId Source code
newResult Man page Source code
newSection Man page Source code
newSubSection Man page Source code
newSubSubSection Man page Source code
newTable Man page Source code
newWebCitation Man page Source code
nitEnvCounter Source code
nitNumbers Source code
nozzle Man page
onLoad Source code
removeElementById Source code
removeProtectedElements Source code
setContactInformation Man page Source code
setCopyright Man page Source code
setCustomPrintCss Man page Source code
setCustomScreenCss Man page Source code
setDoi Man page Source code
setDoiCreator Man page Source code
setDoiPublisher Man page Source code
setDoiResolver Man page Source code
setDoiTitle Man page Source code
setDoiVersion Man page Source code
setDoiYear Man page Source code
setFigureFile Man page Source code
setFigureFileHighRes Man page Source code
setGlobalReportId Source code
setGoogleAnalyticsId Man page Source code
setLogo Man page Source code
setMaintainerAffiliation Man page Source code
setMaintainerEmail Man page Source code
setMaintainerName Man page Source code
setNextReport Man page Source code
setParentReport Man page Source code
setPreviousReport Man page Source code
setReportSubTitle Man page Source code
setReportTitle Man page Source code
setSignificantEntity Man page Source code
setSoftwareName Man page Source code
setSoftwareVersion Man page Source code
setTableFile Man page Source code
tag Source code
trimTable Source code
updateEnvCounter Source code
updateNumberedElements Source code
updateReferences Source code
updateResults Source code
write Source code
writeBottomLogos Source code
writeCitation Source code
writeDoiCitationInformation Source code
writeElement Source code
writeElements Source code
writeFigure Source code
writeGeneralReport Source code
writeHtml Source code
writeJsonCharacter Source code
writeJsonElement Source code
writeJsonList Source code
writeJsonNull Source code
writeJsonNumeric Source code
writeList Source code
writeMaintainerInformation Source code
writeMetaInformation Source code
writeParagraph Source code
writeReport Man page Source code
writeResult Source code
writeSection Source code
writeTable Source code
writeTopLogos Source code

Files

MD5
R
R/nozzle.R
NEWS
NAMESPACE
man
man/writeReport.Rd
man/TABLE.SIGNIFICANT.DIGITS.Rd
man/setTableFile.Rd
man/setSoftwareVersion.Rd
man/setSoftwareName.Rd
man/setSignificantEntity.Rd
man/setReportTitle.Rd
man/setReportSubtitle.Rd
man/setPreviousReport.Rd
man/setParentReport.Rd
man/setNextReport.Rd
man/setMaintainerName.Rd
man/setMaintainerEmail.Rd
man/setMaintainerAffiliation.Rd
man/setLogo.Rd
man/setGoogleAnalyticsId.Rd
man/setFigureFileHighRes.Rd
man/setFigureFile.Rd
man/setDoiYear.Rd
man/setDoiVersion.Rd
man/setDoiTitle.Rd
man/setDoiResolver.Rd
man/setDoiPublisher.Rd
man/setDoiCreator.Rd
man/setDoi.Rd
man/setCustomScreenCss.Rd
man/setCustomPrintCss.Rd
man/setCopyright.Rd
man/setContactInformation.Rd
man/SECTION.CLASS.RESULTS.Rd
man/SECTION.CLASS.META.Rd
man/RDATA.REPORT.Rd
man/PROTECTION.TCGA.Rd
man/PROTECTION.PUBLIC.Rd
man/PROTECTION.PRIVATE.Rd
man/PROTECTION.GROUP.Rd
man/Nozzle.R1-package.Rd
man/newWebCitation.Rd
man/newTable.Rd
man/newSubSubSection.Rd
man/newSubSection.Rd
man/newSection.Rd
man/newResult.Rd
man/newReport.Rd
man/newParameterList.Rd
man/newParagraph.Rd
man/newList.Rd
man/newJournalCitation.Rd
man/newHtml.Rd
man/newFigure.Rd
man/newCustomReport.Rd
man/newCitation.Rd
man/LOGO.TOP.RIGHT.Rd
man/LOGO.TOP.LEFT.Rd
man/LOGO.TOP.CENTER.Rd
man/LOGO.BOTTOM.RIGHT.Rd
man/LOGO.BOTTOM.LEFT.Rd
man/LOGO.BOTTOM.CENTER.Rd
man/isTable.Rd
man/isFigure.Rd
man/IMAGE.TYPE.SVG.Rd
man/IMAGE.TYPE.RASTER.Rd
man/IMAGE.TYPE.PDF.Rd
man/HTML.REPORT.Rd
man/HTML.FRAGMENT.Rd
man/getTableFile.Rd
man/getSummary.Rd
man/getSoftwareVersion.Rd
man/getSoftwareName.Rd
man/getSignificantResultsCount.Rd
man/getSignificantEntity.Rd
man/getReportTitle.Rd
man/getReportSubtitle.Rd
man/getReportId.Rd
man/getRendererName.Rd
man/getRendererDate.Rd
man/getMaintainerName.Rd
man/getMaintainerEmail.Rd
man/getMaintainerAffiliation.Rd
man/getLogo.Rd
man/getGoogleAnalyticsId.Rd
man/getFigureFileHighRes.Rd
man/getFigureFile.Rd
man/getExportedElementIds.Rd
man/getExportedElement.Rd
man/getDoiYear.Rd
man/getDoiVersion.Rd
man/getDoiTitle.Rd
man/getDoiResolver.Rd
man/getDoiPublisher.Rd
man/getDoiCreator.Rd
man/getDoi.Rd
man/getCustomScreenCss.Rd
man/getCustomPrintCss.Rd
man/getCreatorName.Rd
man/getCreatorDate.Rd
man/getCopyrightYear.Rd
man/getCopyrightUrl.Rd
man/getCopyrightStatement.Rd
man/getCopyrightOwner.Rd
man/getContactInformationSubject.Rd
man/getContactInformationMessage.Rd
man/getContactInformationLabel.Rd
man/getContactInformationEmail.Rd
man/DEFAULT.SIGNIFICANT.ENTITY.Rd
man/DEFAULT.REPORT.FILENAME.Rd
man/DEFAULT.DOI.RESOLVER.Rd
man/asValue.Rd
man/asSummary.Rd
man/asStrong.Rd
man/asReference.Rd
man/asParameter.Rd
man/asLink.Rd
man/asFilename.Rd
man/asEmph.Rd
man/asCode.Rd
man/addToSummary.Rd
man/addToResults.Rd
man/addToReferences.Rd
man/addToOverview.Rd
man/addToMethods.Rd
man/addToMeta.Rd
man/addToIntroduction.Rd
man/addToInput.Rd
man/addTo.Rd
inst
inst/js
inst/js/nozzle.min.js
inst/js/nozzle.js
inst/js/jquery.tablesorter.min.js
inst/js/jquery.tablesorter.js
inst/js/jquery-1.5.1.min.js
inst/js/google-analytics.js
inst/css
inst/css/nozzle_with_print.css
inst/css/nozzle.print.min.css
inst/css/nozzle.print.css
inst/css/nozzle.min.css
inst/css/nozzle.css
DESCRIPTION
Nozzle.R1 documentation built on May 19, 2017, 10:54 a.m.