Nozzle.R1-package | Nozzle: a Report Generation Toolkit for Data Analysis Pipelines |
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. |
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 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. |
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 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 |
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 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. |
TABLE.SIGNIFICANT.DIGITS | Default number of significant digits to be used to trim numeric columns in tables. |
writeReport | Write 'report' to file. |