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Nozzle.R1 (version 1.1-1.1)

Nozzle Reports

Description

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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Version

Install

install.packages('Nozzle.R1')

Monthly Downloads

510

Version

1.1-1.1

License

LGPL-2

Issues

Pull Requests

Stars

Forks

Repository

http://github.com/parklab/nozzle

Homepage

http://gdac.broadinstitute.org/nozzle

Maintainer

Nils Gehlenborg

Last Published

June 23rd, 2022

Functions in Nozzle.R1 (1.1-1.1)

LOGO.BOTTOM.CENTER

DEFAULT.DOI.RESOLVER

Default DOI resolver URL.

DEFAULT.REPORT.FILENAME

Default filename for reports.

LOGO.BOTTOM.LEFT

IMAGE.TYPE.RASTER

PROTECTION.TCGA

Group visibility.

DEFAULT.SIGNIFICANT.ENTITY

Name of entities that are labeled as signficiant.

Add elements to the "Meta" section of a standard report.

PROTECTION.PUBLIC

Public visibility.

addToReferences

Add elements to the "References" subsection in the "Methods & Data" section of a standard report.

Add elements to the "Overview" section of a standard report.

Reference a citation, figure or table element.

Format text as parameter.

addToIntroduction

Add elements to the "Introduction" subsection in the "Overview" section of a standard report.

Add elements to the "Input" subsection in the "Methods & Data" section of a standard report.

PROTECTION.PRIVATE

Private visibility.

Add elements to the "Methds & Data" section of a standard report.

Format text as code.

getContactInformationLabel

Get label for contact button for report.

Add child elements to a parent element.

PROTECTION.GROUP

Group visibility.

getContactInformationMessage

Get contact email default message for report.

TABLE.SIGNIFICANT.DIGITS

Default number of significant digits to be used to trim numeric columns in tables.

Nozzle.R1-package

Nozzle: a Report Generation Toolkit for Data Analysis Pipelines

Get the DOI version for report.

Get the DOI year for report.

Format text with emphasis (usually resulting in text set in italics).

getContactInformationEmail

Get contact email address for report.

Format text as value.

getCustomScreenCss

Get the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet.

Get path or URL of image file associated with a figure element.

Format text as filename.

Get the DOI (document object identifier, http://www.doi.org) for report.

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.

Format text as a hyperlink.

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.

getReportSubTitle

Get the subtitle of report.

Get logo file for one of six positions (three at the top, three at the bottom) in report.

Get the first element of the "Summary" subsection in the "Overview" section in a standard report.

Get path or URL of file associatd with table element.

SECTION.CLASS.META

SECTION.CLASS.RESULTS

Test if element is a figure element.

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.

Format text with strong emphasis (usually resulting in text set in bold).

Create a new result element.

Create a new report with pre-defined sections Overview/Introduction, Overview/Summary, Results, Methods & Data/Input, Methods & Data/References and Meta Data.

Include a result in text. This is a legacy method and provided only for backwards compatibility.

LOGO.BOTTOM.RIGHT

setGoogleAnalyticsId

Set the Google Analytics tracking ID to be embedded in this report ("web property id", usually starts with "UA-").

Set a logo file for one of six positions (three at the top, three at the bottom) in report, e.g. an institute logo.

getCopyrightYear

Get copyright year report.

Create a new list element.

Get the title of report.

newJournalCitation

Create a citation element that represents a document published in a journal. This is a convenience wrapper for newCitation.

Test if element is a table element.

Get the DOI creator for report.

LOGO.TOP.CENTER

Add elements to the "Results" section of a standard report.

Get date when report was created.

getContactInformationSubject

Get contact email subject line for report.

getCopyrightOwner

Get name of the copyright owner for report.

Add elements to the "Summary" subsection in the "Overview" section of a standard report.

Set the DOI meta data year for report.

Set the DOI meta data version for report.

getDoiPublisher

Get the DOI publisher for report.

getMaintainerName

Get name of maintainer of report.

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.

Get name and version of the Nozzle package that was used to create report.

Set the DOI meta data creator for report.

setReportSubTitle

Set the subtitle of report.

setDoiPublisher

Set the DOI meta data publisher for report.

setMaintainerName

Set name of maintainer of report.

Set the title of report.

getRendererDate

Get date when report was rendered.

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.

Set the URL and title of the "next" report after report. This will be accessible through the utility menu.

Get the DOI resolver URL (e.g. http://dx.doi.org) for report.

Get the DOI title for report.

Create a citation element.

getCustomPrintCss

Get the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet.

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.

getMaintainerAffiliation

Get affiliation of maintainer of report.

getMaintainerEmail

Get email address of maintainer of report.

Create a new paragraph element.

getRendererName

Get name and version of the Nozzle package that was used to render report.

getExportedElementIds

Get the IDs of exported elements from report. This is an experimental feature of Nozzle and may not lead to the expected results.

newSubSubSection

Create a new subsubsection 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.

Create new table element.

Get the ID (a UUID) of report.

Create a new list element.

Create a new freeform HTML element. THIS MUST BE USED WITH EXTRAORDINARTY CARE!

Create a new section element.

Set path or URL of image file associated with a figure element. Paths can relative or absolute.

setParentReport

Set the URL and title of the "parent" report above report. This will be accessible through the utility menu.

Create a new subsection element.

setPreviousReport

Set the URL and title of the "previous" report before report. This will be accessible through the utility menu.

setFigureFileHighRes

Set path or URL of high-resolution or vector-based image file associated with a figure element. Paths can be relative or absolute.

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".

newCustomReport

Create a new custom report without pre-defined sections.

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.

setMaintainerAffiliation

Set affiliation of maintainer of report.

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.

setMaintainerEmail

Set email address of maintainer of report.

Write report to file.

Create a citation element that represents a document published online. This is a convenience wrapper for newCitation.

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.

Set the DOI meta data title for report.

setSoftwareVersion

Set the name of the software that used Nozzle to generate report, e.g. "Version 1.2".

Set the DOI resolver URL (e.g. http://dx.doi.org) for report. The URL must not end with a slash!

Set path or URL of file associatd with table element.