# Nozzle Reports

## Documentation for package ‘Nozzle.R1’ version 1.1-1.1

- DESCRIPTION file
- Package NEWS

## Help Pages

A D G H I L N P R S T W

Nozzle.R1-package | Nozzle: a Report Generation Toolkit for Data Analysis Pipelines

## -- A --

addTo | Add child elements to a parent element.
addToInput | Add elements to the "Input" subsection in the "Methods & Data" section of a standard report.
addToIntroduction | Add elements to the "Introduction" subsection in the "Overview" section of a standard report.
addToMeta | Add elements to the "Meta" section of a standard report.
addToMethods | Add elements to the "Methds & Data" section of a standard report.
addToOverview | Add elements to the "Overview" section of a standard report.
addToReferences | Add elements to the "References" subsection in the "Methods & Data" section of a standard report.
addToResults | Add elements to the "Results" section of a standard report.
addToSummary | Add elements to the "Summary" subsection in the "Overview" section of a standard report.
asCode | Format text as code.
asEmph | Format text with emphasis (usually resulting in text set in italics).
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 set in bold).
asSummary | Include a result in text. This is a legacy method and provided only for backwards compatibility.
asValue | Format text as value.

## -- D --

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.

## -- G --

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 the copyright URL.
getCopyrightUrl | Get copyright URL for 'report', which is linked to the copyright statement.
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 create 'report'.
getCustomPrintCss | Get the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet.
getCustomScreenCss | Get the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet.
getDoi | Get the DOI (document object identifier, http://www.doi.org) for 'report'.
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 'report'.
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 generate aggregate reports. This is an experimental feature of Nozzle and may not lead to the expected results.
getExportedElementIds | Get the IDs of exported elements from 'report'. This is an experimental feature of Nozzle and may not lead to the expected results.
getFigureFile | Get path or URL of image file associated with a figure element.
getFigureFileHighRes | Get path or URL of high-resolution of vector-based image file associated with a figure element.
getGoogleAnalyticsId | Get Google Analytics tracking ID for 'report'.
getLogo | Get logo file for one of six positions (three at the top, three at the bottom) in 'report'.
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 render 'report'.
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. "gene". This is currently not being used and might become obsolete in future versions of Nozzle.
getSignificantResultsCount | Get the total number of significant results in 'report'.
getSoftwareName | Get the name of the software that used Nozzle to generate 'report'.
getSoftwareVersion | Get the version of the software that used Nozzle to generate 'report'.
getSummary | Get the first element of the "Summary" subsection in the "Overview" section in a standard report.
getTableFile | Get path or URL of file associatd with table element.

## -- H --

HTML.FRAGMENT | Output type.
HTML.REPORT | Output type.

## -- I --

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.

## -- L --

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.

## -- N --

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 EXTRAORDINARTY CARE!
newJournalCitation | Create a citation element that represents a document published in a journal. This is a convenience wrapper for 'newCitation'.
newList | Create a new list element.
newParagraph | Create a new paragraph element.
newParameterList | Create a new parameter list element. A parameter list is an unnumbered list of the form param_1 = value_1, ..., param_n = value_n where param_i is formated as a parameter and value_i is formatted as a value.
newReport | Create a new report with pre-defined sections Overview/Introduction, Overview/Summary, Results, Methods & Data/Input, Methods & Data/References and Meta Data.
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 published online. This is a convenience wrapper for 'newCitation'.
nozzle | Nozzle: a Report Generation Toolkit for Data Analysis Pipelines

## -- P --

PROTECTION.GROUP | Group visibility.
PROTECTION.PRIVATE | Private visibility.
PROTECTION.PUBLIC | Public visibility.
PROTECTION.TCGA | Group visibility.

## -- R --

RDATA.REPORT | Output type.

## -- S --

SECTION.CLASS.META | Section class.
SECTION.CLASS.RESULTS | Section class.
setContactInformation | Set contact information for 'report'. This is used to create a "contact" button in the top right corner of the report, e.g. to collect feedback about the report.
setCopyright | Set copyright messsage for 'report'.
setCustomPrintCss | Set the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet. Can be relative or absolute.
setCustomScreenCss | Set the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet. Can be relative or absolute.
setDoi | Set the DOI (document object identifier, http://www.doi.org) for 'report'. A warning will be emitted if the report has been assigned a DOI before.
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 'report'. The URL must not end with a slash!
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 element. Paths can relative or absolute.
setFigureFileHighRes | Set path or URL of high-resolution or vector-based image file associated with a figure element. Paths can be relative or absolute.
setGoogleAnalyticsId | Set the Google Analytics tracking ID to be embedded in this report ("web property id", usually starts with "UA-").
setLogo | Set a logo file for one of six positions (three at the top, three at the bottom) in 'report', e.g. an institute logo.
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'. This will be accessible through the utility menu.
setParentReport | Set the URL and title of the "parent" report above 'report'. This will be accessible through the utility menu.
setPreviousReport | Set the URL and title of the "previous" report before 'report'. This will be accessible through the utility menu.
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. "gene". This is currently not being used and might become obsolete in future versions of Nozzle.
setSoftwareName | Set the name of the software that used Nozzle to generate 'report', e.g. "My Report Generator Script".
setSoftwareVersion | Set the name of the software that used Nozzle to generate 'report', e.g. "Version 1.2".
setTableFile | Set path or URL of file associatd with table element.

## -- T --

TABLE.SIGNIFICANT.DIGITS | Default number of significant digits to be used to trim numeric columns in tables.

## -- W --

writeReport | Write 'report' to file.