StabilityR
A systems biology tool for network inference, partitioning and visualisation.
Prerequisites
- Unix systems (Linux/Mac) are currently supported. The Windows-friendly version will be realeased soon.
- LEMON graph library version 1.3.1: http://lemon.cs.elte.hu/trac/lemon/wiki/Downloads
Installation
From within the R console:
require(devtools)
install_github('tleja/StabilityR')Example execution
Load the library and an example graph
library(StabilityR)
data(graph_rings)
mat = graph_rings
time = logspace(-3,1,61)Execute the stability functions
res1 = stability(mat=mat, time=time, full=TRUE, type='norm', M=100)
res2 = stability_evaluate(mat=mat, res=res1)
plotStability(res2)
plotStability_VI(res2)
plotStability_heatmap(res2)Visualise the graph
net = forceAtlas2(mat=mat, iterations=4000, plotstep=10, seed=4, ksmax=100)
plotNetwork(mat=mat, pos=net, group=res2$P[,55])See ?stability for more information.