Hello everyone,
I have a matrix based on binary concept as follows,
T1 T2 T3
Gene1 0 1 1
Gene2 1 0 1
.. 0 0 0
.. 0 1 0
Gene nth 0 0 1
I want to make a network using this matrix in R/bioconductor. Please suggest me some package.
Any help will be appreciated.
Thanks..
•
written
by
Abdul Rawoof
Take a look at http://igraph.org/r/. You can find also many tutorials out there.
You could use the igraph R package. For example, given your input matrix, you could turn it into a set of vertices and edges and then plot its network:
> install.packages("igraph")
> library("igraph")
> verts <- data.frame(name=c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5", "T1", "T2", "T3"))
> edges <- data.frame(from=c("Gene1", "Gene1", "Gene2", "Gene2", "Gene4", "Gene5"), to=c("T2", "T3", "T1", "T3", "T2", "T3"))
> g <- graph.data.frame(edges, directed=TRUE, vertices=verts)
> png("graph.png")
> plot(g)
> dev.off()
The file graph.png might look something like this:
•
written
by
Alex Reynolds
if values are between 0 to 1, then what will be the script. can we mention the edge distance.
Essentially the same solution as above, but allows parsing arbitrary tables
install.packages("igraph", "reshape")
library(igraph); library(reshape)
# read input
# could also read from file with read.delim(file_name)
input <- "gene\tT1\tT2\tT3\nG1\t0\t1\t1\nG2\t1\t0\t0\nG3\t0\t0\t0\nG4\t0\t1\t0\nG5\t0\t0\t1"
df <- read.delim(text = input)
# collapse table, select existing edges
df <- melt(df)
df <- df[,df$value>0]
# build graph
e <- data.frame(from = df$gene, to = df$variable)
g <- graph.data.frame(e)
plot(g)
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