Hi all,
I am using igraph package for analyzing Protien protien interaction networks. The problem is i my dataset is having 10,000 nodes and 30,000 interactions. the options available in igraph::plotting are not suitable with my plot. The code which i tried is as below. The problem with my plot is the nodes and edges are mixed up with each other so the visualization is no clear and which nodes are connected with other nodes is not clear.
rm(list=ls())
options(max.print = 1000000000)
library(igraph)
library(network)
read_data <- read.csv("data.csv", header = T)
read_data
df <- data.frame(read_data$dat.X.node1 , read_data$dat.node2)
levels_of_element <- levels(unlist(df[,1:2]))
levels_of_element
num_of_connection <- matrix(match(as.character(unlist(df[,1:2])), levels_of_element),ncol=2)
num_of_connection
graph_object <- graph.data.frame(df, directed = FALSE)
graph_object
net <- network(num_of_connection, directed=FALSE)
set.seed(1)
par(mar=rep(0,4))
plot(net)
and my data.csv file is
dat.X.node1,dat.node2
trpD,trpB
serB,sdaA
pabA,trpA
pabB,trpA
pabA,pabB
serB,glyA
serB,trpB
trpC,trpA
ilvA,trpA
serB,ilvA
trpE,trpB
pabB,trpC
sdaA,trpB
pabA,trpD
trpE,trpD
pabA,trpC
sdaA,trpA
serB,trpA
pabA,trpE
ilvA,glyA
pabB,trpD
trpD,trpC
ilvA,trpB
glyA,trpA
glyA,trpB
pabA,trpB
trpE,trpA
glyA,sdaA
trpD,trpA
Here i just gave the example of which i am trying in my case. Kindly
help me out.