Nozzle Reports

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

Help Pages

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.