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@Vessy
Created October 4, 2016 18:55
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Plotting networks in R - an example how to plot a network and customize its appearance from R using networkD3 library
############################################################################################
############################################################################################
# Plotting networks in R - an example how to plot a network and
# customize its appearance using networkD3 library
############################################################################################
############################################################################################
# Clear workspace
# rm(list = ls())
############################################################################################
# Read a data set.
# Data format: dataframe with 3 variables; variables 1 & 2 correspond to interactions; variable 3 is weight of interaction
edgeList <- read.table("lesmis.txt", header = FALSE, sep = "\t")
colnames(edgeList) <- c("SourceName", "TargetName", "Weight")
# Create a graph. Use simplyfy to ensure that there are no duplicated edges or self loops
gD <- igraph::simplify(igraph::graph.data.frame(edgeList, directed=FALSE))
# Create a node list object (actually a data frame object) that will contain information about nodes
nodeList <- data.frame(ID = c(0:(igraph::vcount(gD) - 1)), # because networkD3 library requires IDs to start at 0
nName = igraph::V(gD)$name)
# Map node names from the edge list to node IDs
getNodeID <- function(x){
which(x == igraph::V(gD)$name) - 1 # to ensure that IDs start at 0
}
# And add them to the edge list
edgeList <- plyr::ddply(edgeList, .variables = c("SourceName", "TargetName", "Weight"),
function (x) data.frame(SourceID = getNodeID(x$SourceName),
TargetID = getNodeID(x$TargetName)))
############################################################################################
# Calculate some node properties and node similarities that will be used to illustrate
# different plotting abilities and add them to the edge and node lists
# Calculate degree for all nodes
nodeList <- cbind(nodeList, nodeDegree=igraph::degree(gD, v = igraph::V(gD), mode = "all"))
# Calculate betweenness for all nodes
betAll <- igraph::betweenness(gD, v = igraph::V(gD), directed = FALSE) / (((igraph::vcount(gD) - 1) * (igraph::vcount(gD)-2)) / 2)
betAll.norm <- (betAll - min(betAll))/(max(betAll) - min(betAll))
nodeList <- cbind(nodeList, nodeBetweenness=100*betAll.norm) # We are scaling the value by multiplying it by 100 for visualization purposes only (to create larger nodes)
rm(betAll, betAll.norm)
#Calculate Dice similarities between all pairs of nodes
dsAll <- igraph::similarity.dice(gD, vids = igraph::V(gD), mode = "all")
F1 <- function(x) {data.frame(diceSim = dsAll[x$SourceID +1, x$TargetID + 1])}
edgeList <- plyr::ddply(edgeList, .variables=c("SourceName", "TargetName", "Weight", "SourceID", "TargetID"),
function(x) data.frame(F1(x)))
rm(dsAll, F1, getNodeID, gD)
############################################################################################
# We will also create a set of colors for each edge, based on their dice similarity values
# We'll interpolate edge colors based on the using the "colorRampPalette" function, that
# returns a function corresponding to a collor palete of "bias" number of elements (in our case, that
# will be a total number of edges, i.e., number of rows in the edgeList data frame)
F2 <- colorRampPalette(c("#FFFF00", "#FF0000"), bias = nrow(edgeList), space = "rgb", interpolate = "linear")
colCodes <- F2(length(unique(edgeList$diceSim)))
edges_col <- sapply(edgeList$diceSim, function(x) colCodes[which(sort(unique(edgeList$diceSim)) == x)])
rm(colCodes, F2)
############################################################################################
# Let's create a network
D3_network_LM <- networkD3::forceNetwork(Links = edgeList, # data frame that contains info about edges
Nodes = nodeList, # data frame that contains info about nodes
Source = "SourceID", # ID of source node
Target = "TargetID", # ID of target node
Value = "Weight", # value from the edge list (data frame) that will be used to value/weight relationship amongst nodes
NodeID = "nName", # value from the node list (data frame) that contains node description we want to use (e.g., node name)
Nodesize = "nodeBetweenness", # value from the node list (data frame) that contains value we want to use for a node size
Group = "nodeDegree", # value from the node list (data frame) that contains value we want to use for node color
height = 500, # Size of the plot (vertical)
width = 1000, # Size of the plot (horizontal)
fontSize = 20, # Font size
linkDistance = networkD3::JS("function(d) { return 10*d.value; }"), # Function to determine distance between any two nodes, uses variables already defined in forceNetwork function (not variables from a data frame)
linkWidth = networkD3::JS("function(d) { return d.value/5; }"),# Function to determine link/edge thickness, uses variables already defined in forceNetwork function (not variables from a data frame)
opacity = 0.85, # opacity
zoom = TRUE, # ability to zoom when click on the node
opacityNoHover = 0.1, # opacity of labels when static
linkColour = edges_col) # edge colors
# Plot network
D3_network_LM
# Save network as html file
networkD3::saveNetwork(D3_network_LM, "D3_LM.html", selfcontained = TRUE)
################################################################################
# sessionInfo()
#
# R version 3.3.1 (2016-06-21)
# Platform: x86_64-redhat-linux-gnu (64-bit)
# Running under: Fedora 24 (Workstation Edition)
#
# locale:
# [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
# [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
# [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
# [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# loaded via a namespace (and not attached):
# [1] htmlwidgets_0.7 plyr_1.8.4 magrittr_1.5 htmltools_0.3.5 tools_3.3.1 igraph_1.0.1
# [7] yaml_2.1.13 Rcpp_0.12.7 jsonlite_1.1 digest_0.6.10 networkD3_0.2.13
#
################################################################################
@urwa
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urwa commented Jul 4, 2018

Perfect! Thanks a bunch!

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