t-SNE
This software computes the t-SNE distribution map of an unlimited number of files. Computations are based on the t-SNE R package and parallelization is done with GNU parallel.
Manual :
1- if not already installed, install Perl free programming language
2- install R programming language and t-SNE.
install.packages("tsne")
3- install GNU parallel (GNU Linux only)
4- unzip the software
5- copy data tsv files (TAB separator) in the “data” directory :
- first line : columns names
- first column : categories
example :
categorie ABCB1
NK 7.6 7.6
NK 7.6 7.7
T_CD4 5.6
T_CD4 5.15
next columns are the values, with separator TAB.
6 - edit conf.txt to set the number of parameters
7- edit t-SNE-003.r to set your t-SNE parameters
8- execute the software by the command : perl parallel_tsne-0.1.pl
9- plots are in the "svg" directory