Installation¶

Python installation¶

Installation with pip¶

The Python version of PHATE can be installed using:

pip install --user phate

Installation from source¶

The Python version of PHATE can be installed from GitHub by running the following from a terminal:

git clone --recursive git://github.com/KrishnaswamyLab/PHATE.git
cd Python
python setup.py install --user

MATLAB installation¶

The MATLAB version of PHATE can be accessed using:

git clone git://github.com/KrishnaswamyLab/PHATE.git
cd PHATE/Matlab

Add the PHATE/Matlab directory to your MATLAB path and run any of our test scripts to get a feel for PHATE.

R installation¶

In order to use PHATE in R, you must also install the Python package.

Installation from CRAN and PyPi¶

Install phateR from CRAN by running the following code in R:

install.packages("phateR")

Install phate in Python by running the following code from a terminal:

pip install --user phate

Installation with devtools and reticulate¶

The development version of PHATE can be installed directly from R with devtools:

if (!suppressWarnings(require(devtools))) install.packages("devtools")
devtools::install_github("KrishnaswamyLab/phateR")

If you have the development version of reticulate, you can also install phate in Python by running the following code in R:

devtools::install_github("rstudio/reticulate")
reticulate::py_install("phate")

Installation from source¶

The latest source version of PHATE can be accessed by running the following in a terminal:

git clone --recursive git://github.com/KrishnaswamyLab/PHATE.git
cd PHATE/phateR
R CMD INSTALL
cd ../Python
python setup.py install --user

If the phateR folder is empty, you have may forgotten to use the –recursive option for git clone. You can rectify this by running the following in a terminal:

cd PHATE
git submodule init
git submodule update
cd phateR
R CMD INSTALL
cd ../Python
python setup.py install --user