Several R libraries  exist that can be used to generate reports for analysis pipelines. R2HTML

) 
are low-level libraries for writing HTML files. Sweave

and related tools for reproducible research can be used to generate
PDF or HTML documents from within R scripts. However, none of these tools 
provide support in generating reports with dynamic user interface components 
for the presentation of extensive and complex analysis results. To address 
these limitations, we have developed the Nozzle R package, which supports 
pipeline developers in creating comprehensive and user-friendly HTML reports 
to describe the results of analysis pipelines.

Nozzle reports are generated bottom-up (

): in Phase 1 report elements are
generated - e.g. a table and a paragraph of text, in Phase 2 they are assembled
into larger structures - e.g. the table and the paragraph are added to a titled
section, which is added to the report, and in Phase 3 the report is rendered
into HTML.

Sample R script to create a basic Nozzle report that illustrates the three phases of the bottom-up approach. See

A basic Nozzle report generated with the R script shown in Figure 1. All sections and subsections are expanded. The table is sorted ascendingly by "Sepal.Length". The table can be sorted by other variables by clicking on the corresponding column headers.

The guiding principle for the design of the Nozzle package is to enable report
authors - usually pipeline developers - to focus on the content rather than on
the layout or generation of the report. We achieve this through the high-level R
API that enables authors to create report elements such as figures, tables,
paragraphs of text, bibliographic or web references, lists, sections and
subsections using regular R commands without knowledge of the technologies used
for the presentation of the final report.

Nozzle reports provide a rich user interface (

). All figures support
dynamic switching between a thumbnail view and a detail view. They also have a
caption and can be linked to a high-resolution or PDF version of the figure. All
tables are sortable and support automatic trimming of floating point numbers to
a user-defined number of significant digits. Tables also include a caption and
can be linked to external files that contain additional information. Text and
the content of table cells can be marked up semantically using the
Nozzle-specific