This repository contains R and Matlab code related to the following paper:

Stability driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks

by Siqi Wu, Antony Joseph, Ann S. Hammonds, Susan E. Celniker, Bin Yu and Erwin Frise

http://www.pnas.org/cgi/doi/10.1073/pnas.1521171113

See http://insitu.fruity.org/downloads for data.

We assume that the necessary data files (*.csv) are stored in ../ . If you download our data to a different location, please modify the paths accordingly in our files.

Our R and Matlab code admits a few experimental usages and has not been extensively tested. Please email brothercutter@gmail.com to report bugs.



Matlab code 

staNMF_genDicts.m generates dictionaries of different sizes. Since the program takes a long time to run, the results are already stored in ./staNMFDicts/K=* as .mat files.

staNMF_chooseK.m computes the instability quantity to choose the rank of NMF.

staNMF_bestDict.m finds the dictionary with the lowest objective function value given the rank selected by staNMF_chooseK.m.


R code

The file tutorial.R contains examples for displaying and analyzing spatial gene expression in Drosophila embryos.

lasso_nls.R performs the LASSO+NLS procedure described in our paper. It generates sPP coefficients that are identical to those in sPPcoefPatterns.csv.

sPPAnalysis.R analyzes sPP coefficients.

SLCN.R produces spatially local correlation networks.