mito-network-sharing

Sharing of contents on mitochondrial encounter networks

Required: R with igraph, brainGraph, ggplot2, and XML libraries; igraph libraries for C

igraph can be a pain to install for C. See bingo.c below for how to optionally run the code without this dependency.

Wrapper scripts

runcode.sh calls R code to extract encounter networks from XML trajectory information in Data/, then C code to generate other networks for comparison and simulate the "bingo" game on these.

plots.R calls R code to produce summary plots of the results.

Code

trajectory-analysis.R extracts encounter networks from XML files and imposes any required restrictions (for example, truncating trajectory lengths)

bingo.c is the workhorse C code for network generation and "bingo" simulation. For full functionality, this needs the igraph library. However, a preprocessor directive within the code can be removed, removing the igraph dependency. In this case, zeroes are output for all network statistics that igraph would provide. The followup R code can be used to compute these statistics for a subset of the networks generated in the simulations.

The various bingo-...-script.R scripts produce visualisations of the different aspects of the simulations.