SPADE: Spanning Tree Progression of Density Normalized Events
SPADE is a visualization and analysis tool for high-dimensional flow cytometry data. SPADE is implemented as an R package and can be installed via R's packaging facilities. Additionally a GUI is provided, as a Cytoscape plugin, for setting-up and interactively visualizing the results of SPADE analyses. Please see the project homepage at cytospade.org or the wiki for the primary documentation.
User Setup
Please refer to the wiki pages, especially the Getting Started page.
Developer Setup
Prerequisites
- Latest version of R
- igraph
- flowCore
Building and Installing
The SPADE package has a C++ core that must be built before use. SPADE successfully builds on Linux, OSX and Windows (with Rtools), although Windows users will not be able to take advantage of the OpenMP parallelization used within SPADE. SPADE can be installed from the command line via
$ R CMD INSTALL <SPADE PATH>On Windows, you will need to install the Rtools that matches your R distribution. (Important note: if you're using R 2.14, you should use Rtools 2.15. Even though Rtools 2.14 is listed as compatible, it requires extra work to make g++ work. Rtools 2.15 works out of the box.) After installation make sure that your PATH contains the neccessary Rtools binary directories, e.g.:
Open Control Panel -> System
Click on Advanced Tab and then on Environment Variables
Highlight PATH and click Edit
In the character string in Variable Value, make sure the following appear (before other/older compilers):
c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\gcc-4.6.3\bin;c:\Rtools\MinGW\bin;c:\Program Files\R<your R version>\bin;
Building Packages
Source packages can be built with
$ R CMD build <SPADE PATH>and binary packages with
$ R CMD build --no-vignettes --binary <SPADE PATH>Tips and Resources
Citations
SPADE was developed in the Plevritis and Nolan Labs at Stanford University, and is described in the following publications:
- Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP, "CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data". Bioinformatics, 2012.
- Peng Qiu, Erin F. Simonds, Sean C. Bendall, Kenneth D. Gibbs, Robert V. Bruggner, Michael D. Linderman, Karen Sachs, Garry P. Nolan, Sylvia K. Plevritis, "Phenotypically determined self-organization of flow cytometry data with spanning-tree progression analysis of density normalized events". Nature Biotechnolgy, 2011.
- Sean C. Bendall, Erin F. Simonds, Peng Qiu, El-ad D. Amir, Peter O. Krutzik, Rachel Finck, Robert V. Bruggner, Rachel Melamed, Angelica Trejo, Olga I. Ornatsky, Robert S. Balderas, Sylvia K. Plevritis, Karen Sachs, Dana Pe’er, Scott D. Tanner, Garry P. Nolan, "Single-Cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum", Science, 332 (6030): 687-696.
- Michael D. Linderman, Erin F. Simonds, Peng Qiu, Zach Bjornson, Nikesh Kotecha, Teresa H. Meng, Sylvia Plrevritis, Garry P. Nolan, "Algorithmically recovering the hematopoietic lineage from high-dimensional cytometry data using SPADE", Congress of the Intl. Society for Advancement of Cytometry, 2010.