> ####################################################################
> # LAB 9: Converting igraph to SoNIA with R
> ####################################################################
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> # NOTE: if you have trouble because some packages are not installed,
> # see lab 1 for instructions on how to install all necessary packages.
> # Also see Lab 1 for prior functions.
> Ê
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> ##############################################################
> # SoNIA visualizes networks based on vertex and edge (arc) data.
> # A number of variables commonly used in iGraph graph objects
> # directly map to SoNIA counterparts.  At minimum, SoNIA requires:
> # Vertex ids and an edgelsit of directed interactions.
> #
> # Note: For clarity, the iGraph terms Vetex and Edge are used in
> # this lab in place of SoNIA's node and arc.
> ##############################################################
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> ###
> # 1. SET UP SESSION
> ###
> 
> library('igraph')
> library("igraphtosonia")
> setwd("/Users/seanwestwood/Desktop/graph.to.sonia")
> 
> #################################################################
> # SoNIA requirements
> # For vertex (node) entires, we must supply:
> #
> #
> # NodeId - must be an integer. values can be used more than once 
> #	(to specify changes in a node's attributes over time) BUT 
> #	MUST FORM A CONTINUOUS SEQUENCE. (if you try to leave out 
> #	numbers it will throw an error, as this would mess up the 
> #	matrix references.
> #
> # Additionally, the following vetex attirbutes are supported by 
> # the igraphToSoNIA package:
> #
> # Label - text to be displayed as the vertex label.
> # ColorName - text specifying a color for the vertex, one of: 
> #	Black DarkGray LightGray White Cyan Green Magenta Orange 
> #	Pink Red Yellow Blue 
> # NodeShape - text specifying the shape for the node, current 
> #	can only be "ellipse" or "rect"
> # NodeSize - positive real number specifying the size of the 
> #	vertex in pixels
> # StartTime - real value specifying the start time for the node
> # EndTime - real value specifying the end time for the node. 
> #
> #
> #
> # For edge (arc) entires, we must supply: 
> #
> # FromId - integer (or string, if aplpha id is used) 
> #	indicating the ego node must match with a vetext (node) id
> # ToId - integer indicating the alter node must match 
> #	with a vetext (node) id
> #    
> # Additionally, the following edge attirbutes are supported by 
> # the igraphToSoNIA package:   
> #
> # ArcWeight - real value indicating the strength of the relation
> # ArcWidth - real value indicating how wide to draw the arrow
> # ColorName text specifying a color for the edge, one of: 
> #	Black DarkGray LightGray White Cyan Green Magenta Orange 
> #	Pink Red Yellow Blue. 
> # StartTime - real value indicating 
> #	the edge's start
> # EndTime - real value indicating the edge's termination 
> #################################################################
> 
> # The first step is to create an iGraph graph object.  In practice,
> # this code is most useful if you already have an iGraph graph you wish
> # to visualize with SoNIA
> 
> edgelist <- read.csv('edges.csv',header=T)
> attributes <- read.csv("vertices.csv",header=T)
> graph <- graph.data.frame(d= edgelist, directed=T, vertices = attributes)
> 
> #################################################################
> # Important
> # If some of the optional attirbues are not present in your 
> # data comment out the entry to remove the attribute from your 
> # export and to instruct SoNIA to use the default value
> #################################################################
> 
> # Set required vertex attribute
> 
> # set node label
> V(graph)$label <- V(graph)$name
> 
> # Set optional vertex attributes.  If we will not use a vertex 
> # attribute in SoNIA, we will set the attribute to NA
> 
> # set vertex color (named colors per the list above)
> V(graph)$frame.color = c("red","blue","gray")[V(graph)$polticalparty]
> 
> # set vertex shape (circle and rectangle only)
> V(graph)$shape = c("circle","rectangle")[V(graph)$gender]
> V(graph)$frame.shape = V(graph)$shape
> 
> # set vertex size
> V(graph)$vertex.size =10
> 
> # if we do not have individual start and end times for the nodes, 
> # do not set a value for these nodes by commenting out the following lines
> # values of 0 and 30 will display all vertices at all times in SoNIA
> # set start time for the node
> V(graph)$start.time <-1
> 
> # set end time for the node
> V(graph)$end.time <-6
> 
> 
> # The fromId and toId will be set by igraph to sequential values 
> # by default. If V(graph)$label is used, then the ids will be strings 
> # corresponding to the value set.
> 
> # set optional edge attributes
> 
> # set start time for the edge 
> E(graph)$start.time <-E(graph)$start
> 
> # set end time for the edge
> E(graph)$end.time <-E(graph)$start
> 
> # set edge weight
> E(graph)$weight <- runif(ecount(graph))
> 
> # set the edge arrow width
> 
> E(graph)$arrow.size=1.6
> 
> # set edge color (named colors per the list above)
> E(graph)$color = "blue"
> 
> # create the .son output
> write.graph.to.sonia(graph,"export.son")
[1] "file exported"
> 
> # when you load the file in SoNIA you MUST rescale the layout.  It will
> # look as if nothing was loaded, but it is just a bug in SoNIA. "Rescaling
> # layout to fit window" will fix the issue. 
> 
> 
>