Re: [igraph] Fwd: Large network plots in igraph

[Gábor Csárdi]

I guess you need a bigger figure.

But most networks of that size are impossible to meaningfully
visualize, anyway, imo. You need to simplify it, e.g. find clusters in
it, and then visualize the clusters.

Gabor

On Sun, Sep 13, 2015 at 3:11 PM, seema aswani <address@hidden> wrote:
>
> ---------- Forwarded message ----------
> From: seema aswani <address@hidden>
> Date: Sun, Sep 13, 2015 at 4:54 PM
> Subject: Large network plots in igraph
> To: Help for igraph users <address@hidden>, Gábor Csárdi
> <address@hidden>
>
>
> 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.
>
>
>
>
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