GitHub - ryanbressler/GraphSpectrometer: Scripts and utilities for analyzing graphs using Fiedler vectors and spectral graph theory.

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Scripts and utilities for analyzing graphs using Fiedler vectors and spectral graph theory.

www.systemsbiology.org/

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Name		Name	Last commit message	Last commit date
Latest commit History 273 Commits
GraphSpectrometer.js		GraphSpectrometer.js
LICENSE		LICENSE
README		README
allPW.sh		allPW.sh
allRF.sh		allRF.sh
allRFPred.sh		allRFPred.sh
annotateForPredPower.py		annotateForPredPower.py
annotateLeaves.py		annotateLeaves.py
apendixD3plot.py		apendixD3plot.py
branchMatrix.py		branchMatrix.py
comparisonPlot.py		comparisonPlot.py
ctddtompPlot.py		ctddtompPlot.py
d3plot.py		d3plot.py
errorrate.sh		errorrate.sh
fiedler.py		fiedler.py
fiedlerservice.py		fiedlerservice.py
fold_fm.py		fold_fm.py
goerrorrate.sh		goerrorrate.sh
hypergeom.py		hypergeom.py
leafAnalysis.sh		leafAnalysis.sh
mean.py		mean.py
mergedata.py		mergedata.py
parseByCol.py		parseByCol.py
parseRfPred.py		parseRfPred.py
plotClusts.py		plotClusts.py
plotjson.py		plotjson.py
plotjsondecomp.py		plotjsondecomp.py
plotpredDecomp.py		plotpredDecomp.py
predict.sh		predict.sh
pruneLeaves.py		pruneLeaves.py
rfwithdefaults.sh		rfwithdefaults.sh
runMDS.py		runMDS.py
runMDS.sh		runMDS.sh
runSingleRfAndLeaves.sh		runSingleRfAndLeaves.sh
runall.sh		runall.sh
runleafcount.sh		runleafcount.sh
runpw.sh		runpw.sh
runpwcomps.sh		runpwcomps.sh
runrf.sh		runrf.sh
runrf_no_bl.sh		runrf_no_bl.sh
runsplitcount.sh		runsplitcount.sh
setvars.sh		setvars.sh
subset_fm.py		subset_fm.py
summarizeVectors.py		summarizeVectors.py

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GraphSpectrometer

A set of python/numpy scripts and utilities for using fiedler vectors and discrete exterior calculus to layout, analize and visualize large graphs.

Dependecies:
http://code.google.com/p/pyamg/
http://code.google.com/p/pydec/

Slides explaining math and example output:
https://docs.google.com/presentation/d/1uUtt7kVcQtESLISqiNzVMqbsbzcNn09P1q37QBFCeiQ/edit

See doc strings in code for usage for now