A paper describing the package was published in Bioinformatics. Please cite this paper if you are using Nozzle in your work:
N Gehlenborg, MS Noble, G Getz, L Chin and PJ Park, "Nozzle: a report generation toolkit for data analysis pipelines", Bioinformatics 29:1089-1091 (2013)
About the Name
The package was orignally developed for a data analysis pipeline called "Firehose" and the name "Nozzle" was chosen because the package is used to focus the output of Firehose. The "R1" in the "Nozzle.R1" package name stands for "revision 1" of the Nozzle R API. All versions of the Nozzle.R1 package will be backwards-compatible and able to render reports generated with earlier versions of the package. When backwards-compatibility of the API can no longer maintained the package name will change to "Nozzle.R2".
Obtaining and Installing the R package
As of version 1.0-0 the R package is available from CRAN and can be installed directly from R:
install.packages( "Nozzle.R1", type="source" );
The package can also be downloaded from the Nozzle site at the Broad Institute. The package has no external dependencies and can be installed by calling the following from the command line:
R CMD install Nozzle.R1
Creating a Basic Report
The following code creates a report with one section and two subsections. The first subsection contains a table and the second subsection contains a paragraph of text:
require( Nozzle.R1 ) # Phase 1: create report elements r <- newCustomReport( "My Report" ); s <- newSection( "My Section" ); ss1 <- newSection( "My Subsection 1" ); ss2 <- newSection( "My Subsection 2" ); f <- newTable( iris[45:55,], "Iris data." ); # w/ caption p <- newParagraph( "Some sample text." ); # Phase 2: assemble report structure bottom-up ss1 <- addTo( ss1, f ); # parent, child_1, ..., child_n ss2 <- addTo( ss2, p ); s <- addTo( s, ss1, ss2 ); r <- addTo( r, s ); # Phase 3: render report to file writeReport( r, filename="my_report" ); # w/o extension
Two files called
my_report.RData will be written to the current working directory.
An comprehensive demo that uses almost the complete Nozzle API is in the
demo.R file and the
demo.css file are required for the example to work. The rendered HTML reports can be viewed on the Nozzle site at the Broad Institute.
Building the R package
Nozzle works with R 2.10 or later. Use standard R commands to build the package in the cloned repo directory:
R CMD check Nozzle.R1 R CMD build Nozzle.R1
The Nozzle API is documented using the
roxygen2 R package. To rebuild the Rd files in the
man directory run the following from the R shell (using the cloned repo directory as the working directory):
library(methods); library(utils); library(roxygen2); roxygenize("Nozzle.R1", copy=FALSE);
inst directory you need to download the YUI compressor and run the following from the command line:
java -jar Tools/yuicompressor-2.4.2.jar -o Nozzle.R1/inst/js/nozzle.min.js Nozzle.R1/inst/js/nozzle.js java -jar Tools/yuicompressor-2.4.2.jar -o Nozzle.R1/inst/css/nozzle.print.min.css Nozzle.R1/inst/css/nozzle.print.css java -jar Tools/yuicompressor-2.4.2.jar -o Nozzle.R1/inst/css/nozzle.min.css Nozzle.R1/inst/css/nozzle.css
Nozzle was developed with funding from The Cancer Genome Atlas program of the National Cancer Institute, U24 CA143867.