sirusb

The range sliders at the top change the values for the force-directed algorithm and the buttons load new graphs and apply various techniques. This will hopefully serve as a tool for teaching network analysis and visualization principles during my Gephi courses and general Networks in the Humanities presentations.

Notice this includes a pretty straightforward way to load CSV node and edge lists as exported from Gephi.

It also includes a pathfinding algorithm built for the standard data structure of force-directed networks in D3. This requires the addition of .id attributes for the nodes, however.

Now with Clustering Coefficients!

Also, it loads images for nodes but the images are not in the gist. The code also refers to different network types but the data files on Gist only refer to the transportation network.

	# see How to Install Redis Server on CentOS 7 - http://linoxide.com/storage/install-redis-server-centos-7/

	# --- Compiling ---
	$ yum install gcc make tcl
	$ REDIS_VER=3.2.3
	$ wget http://download.redis.io/releases/redis-$REDIS_VER.tar.gz
	$ tar xzvf redis-$REDIS_VER.tar.gz
	$ cd redis-$REDIS_VER
	$ make
	$ make test

	doInstall <- TRUE # Change to FALSE if you don't want packages installed.
	toInstall <- c("ggplot2", "reshape2", "RColorBrewer")
	if(doInstall){install.packages(toInstall, repos = "http://cran.us.r-project.org")}
	lapply(toInstall, library, character.only = TRUE)

	# Generate a random matrix
	# This can be any type of numeric matrix,
	# though we often see heatmaps of square correlation matrices.
	nRow <- 9
	nCol <- 16

	# Load the BSgenome package and download the hg19 reference sequence
	# For documentation see http://www.bioconductor.org/packages/release/bioc/html/BSgenome.html
	source("http://www.bioconductor.org/biocLite.R")
	biocLite("BSgenome")
	biocLite("BSgenome.Hsapiens.UCSC.hg19") #installs the human genome (~850 MB download).

	library('BSgenome.Hsapiens.UCSC.hg19')

	# Function to pull flanking sequence. Defaults to +/- 10 bp
	getflank <- function(position, alleles="[N/N]", chr="chr12", offset=10) {