This software provides the source code of the R package flowPeaks
The printer friendly version of this file is part of the vignette pdf file
located at flowPeaks/inst/doc/flowPeaks-guide.pdf in the source package or
located at flowPeaks/doc/flowPeaks-guide of the installed flowPeaks library
or Windows built library.
Under the Artistic License, you are free to use and redistribute
this software. However, we ask you to cite the following paper if
you use this software for publication
Ge and Sealfon, flowPeaks: a fast unsupervised clustering for
flow cytometry data via K-means and density peak finding,
Bioinformatics, 2012, In Press
We combine the ideas from the finite mixture model and histogram spatial
exploration together to find the clustering of the flow cytometry data.
This new algorithm, in which we called flowPeaks, can be applied to
high dimensional data and identify irregular shape clusters.
The algorithm first uses K-means algorithm with a large K to partition
the population into many compact clusters. These partitioned data allow
us to generate a smoothed density function. All local peaks are
exhaustively found by exploring the density function and the
cells are clustered by the associated local peak. The algorithm fowPeaks is
automatic, fast and reliable and robust to the cluster shape and outliers.
Details can be seen in the paper by Ge (2012).
3.1 All users
When you are reading this and find the R package is already available in
the Bioconductor package repository. You can install it directly from
--Windows users: select the menu "Packages" and then click
"Select repositories..." and choose "BioC software". And then
select the menu "Packages", click "install R package(s)..." and
then look for the package flowPeaks
--Linux users: This also works for Windows users.
Type the following after you have invoked R
If this succeeds, congratulations.
3.2 Windows Users
Please read section 3.1 to install the R package from Bioconductor
before proceeding this. If you have the prebuilt binary of flowPeaks zip file,
you can install the package by selecting the menu "Packages", and then
"Install packages from a local zip file", and then point to prebuilt binary
of flowPeaks zip file.
To build flowPeaks from the source by using Rtools is very not
straightforward. R novices are not encouraged to try this.
Experienced R users need to carefully follow the instruction of
the Rtools (http://www.murdoch-sutherland.com/Rtools/) and
The GSL library needs to be downloaded from the file local215.zip
The top folder (top_path_local) of the extracted file
local215.zip should contain three subfolders:
include, share and lib. The next step is to modify the file
flowPeaks/src/Makevar.win as below.
PKG_LIBS += -L(top_path_local)/lib/$(R_ARCH)/ -lgsl -lgslcblas -lm
PKG_CXXFLAGS += -I(top_path_local)/include
The users are not encouraged to compile their own gsl library
by MinGW or Visual Studio. Most likely their own version of gsl library
is not going to work.
3.3 Linux Users
To build the flowPeaks package from the source, make sure that the following
is present on your system.
GNU Scientific Library (GSL)
A C++ compiler is needed to build the package as the core function is
coded in C++. GSL can be downloaded directly from
http://www.gnu.org/software/gsl/ and follow its instructions to
install the GSL from the source code. Alternatively, GSL can also be
installed from your linux specific package manager (for example,
Synaptic Package Manager for Ubuntu system). Other than the GSL
binary library, please make sure the GSL development package is
also installed, which includes the header files when building
flowPeaks package. Now you are ready to install the package:
R CMD INSTALL flowPeaks_x.y.z.tar.gz
If GSL is installed at some non-standard location such that it cannot be
found when installing flowPeaks. You need to do the following
1. Find out the GSL include location (<path-to-include>) where the GSL
header files are stored in the sub folder gsl, and GSL library location
(<path-to-lib>) where the lib files are stored. If the GSL's gsl_config
can be run, you can get them easily by gsl-config --cflags
and gsl-config --libs
2. In the file flowPeaks/src/Makevars, you may need to change the last
two lines as below
PKG_CXXFLAGS = -I<path-to-include>
PKG_LIBS = -L<path-to-lib>