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Nozzle R Package
- Firehose Reports At-a-Glance (a visual overview of Nozzle report features)
- API Overview (v1.3-0)
- API Overview (CRAN)
- Preprint of the Nozzle Bioinformatics Applications Note as a Nozzle Report (demonstrates custom styles).
- Advanced demo rendered to HTML (use navigation in the top left corner to navigate to additional reports).
- Firehose Analysis reportsfrom 24 October 2012 (click on "Browse" in the "HTML" column). Here are some highlights:
- Glioblastoma Multiforme Copy Number Analysis with GISTIC2: Demonstrates figures, tables and supplementary information.
- Lung Squamous Cell Carcinoma Gene Mutation Analysis: Demonstrates figures in supplementary information.
- Ovarian Serous Cystadenocarcinoma Putative microRNA Target Analysis: Demonstrates use of citations and input parameter lists in the Methods & Data section.
- Uterine Corpus Endometrioid Carcinoma mRNA CNMF Clustering: Demonstrates (experimental) "Print" feature and "Report an Issue" button in the utility menu bar.
- A very basic example from the GitHub repository.
- The advanced demo requires download of code and additional files to generate the demo reports. Demonstrates all Nozzle features.
- A Nozzle report mimicking a journal paper preprint. Uses a custom style sheet.
Download and Installation
Nozzle is available on CRAN and can be installed directly from the R shell.
For reference only. As of version 1.0-0 Nozzle should be obtained from CRAN. Please note that the releases before 1.0-0 do not contain any documentation within the R package.
The GitHub repository for Nozzle is at http://github.com/parklab/nozzle.
Nozzle is open source software and licensed under the LGPL version 2.1.
All questions related to Nozzle should be sent directly to Nils Gehlenborg (email@example.com). Questions about Nozzle related to the Firehose Analysis pipeline should be directed to firstname.lastname@example.org.
Nozzle & Firehose
Nozzle Reports for Monthly TCGA Firehose Analysis Runs
- Dashboard (public reports available starting January 2012)
Guidelines for Firehose Developers
- Report Guidelines for Firehose Pipeline Developers
Technical Notes on Integrating Nozzle into Firehose Modules
- The path to nozzle libraries can be passed into your R script using the special variable in your manifest/hydrant.deploy file: <nozzle.path> (evaluates to /xchip/tcga/Tools/Nozzle/v1.current). In other words, Firehose will take care of providing this value without the need to expose it to the task configuration (just like <libdir>).
- To load the libraries in R: require("Nozzle.R1", lib.loc=nozzlePath, quietly=TRUE); Where nozzlePath is a variable passed into the R script containing <nozzle.path>.
- All the resources referenced in your report must be in the top directory. For example, nesting of directories for figure image files will not display correctly in the Firehose UI.
- The report must be named nozzle.html. This is the default file name produced by writeReport(myReport). However, writeReport(myReport, filename="report.html") will not work.
- In some cases, use of the <R> variable in the manifest/hydrant.deploy file has caused problems. When to use <R> and when to use a direct path to Rscript is currently unclear.