FIt-SNE Installation

[DillonHammill]

FIt-SNE is supported in CytoExploreR, but requires some additional configuration steps in order to work correctly. These platform-specific configurational steps are outlined below:

Windows

1. Download the windows binary from this link.
2. Extract the contents of the downloaded zip folder to C:/bin.

NOTE: CytoExploreR will automatically look for the FIt-SNE executable on your windows machine. No further configuration is required.

Linux

1. Copy and paste the following into the terminal to download the required FFTW libraries and compile the FIt-SNE code:

# Download required tools
apt-get update && apt-get install -y wget unzip make g++ automake autoconf

# Download FFTW
cd /. &&\
wget http://www.fftw.org/fftw-3.3.8.tar.gz &&\
tar -zxvf fftw-3.3.8.tar.gz &&\
rm -rf fftw-3.3.8.tar.gz &&\
cd fftw-3.3.8 &&\
./configure &&\
make &&\
make install

# Download and install FIt-SNE - (path to FItSNE executable ./FItSNE/FItSNE)
mkdir temp &&\
cd temp &&\
wget --no-check-certificate -O FIt-SNE.zip https://github.com/KlugerLab/FIt-SNE/archive/master.zip &&\
unzip FIt-SNE.zip &&\
rm -rf FIt-SNE.zip &&\
cd FIt-SNE-master &&\
g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp  -o bin/fast_tsne -pthread -lfftw3 -lm -Wno-address-of-packed-member &&\
cd ../ &&\
mv FIt-SNE-master ../FIt-SNE &&\
cd ../ &&\
rm -R temp

Mac

1. Copy and paste the following into the terminal to download the required FFTW libraries and compile the FIt-SNE code:

# Download and install FFTW
mkdir temp &&\
cd temp &&\
curl -O http://www.fftw.org/fftw-3.3.8.tar.gz &&\
gunzip -c fftw-3.3.8.tar.gz | tar xopf - &&\
cd fftw-3.3.8 &&\
./configure && make &&\
sudo make install &&\
cd ../.. &&\
rm -R temp

# Download and install FIt-SNE - (path to FItSNE executable ./FItSNE/FItSNE)
mkdir temp &&\
cd temp &&\
curl -LO https://github.com/KlugerLab/FIt-SNE/archive/refs/heads/master.zip &&\
unzip master.zip &&\
cd FIt-SNE-master &&\
g++ -std=c++11 -O3  src/sptree.cpp src/tsne.cpp src/nbodyfft.cpp  -o bin/fast_tsne -pthread -lfftw3 -lm -Wno-address-of-packed-member &&\
cd ../ &&\
mv FIt-SNE-master ../FIt-SNE &&\
cd ../ &&\
rm -R temp

NOTE: CytoExploreR does not search for FIt-SNE on linux or mac. You will need to manually supply the path to the fast_tsne.R file to the fast_tsne_path argument in cyto_map. See below:

# Map 50000 pooled T Cells events
gs_map <- cyto_map(gs,
                   parent = "T Cells",
                   display = 50000,
                   type = "FIt-SNE",
                   fast_tsne_path = "~/temp/FIt-SNE-master/bin/fast_tsne")