Trend line and slope (R) - r

Question

I'm trying to study this protein interaction net. I need to do a plot of the degree distribution of the edges (last lines of the code), but I'm not able to make a trend line and the slope (last line of the code). Can someone help me please?
install.packages("igraph")
library("igraph")
tfile<-tempfile()
download.file("http://pdg.cnb.uam.es/pazos/tmp/Yeast_int.txt", tfile)
datosraw <- subset(read.delim(tfile, sep="\t", header=F, stringsAsFactors = F), !is.na(V3) & V3!="" & V3!="METHOD")
names(datosraw)<-c("orf1","orf2","method")
datos<-split(datosraw,datosraw$method)
df.y2h <- graph.data.frame(d = datos$Y2H[1:5125,c(1,2)], directed = FALSE)
deg.dist.df.y2h <- degree.distribution(df.y2h)
plot(deg.dist.df.y2h, xlab="k", ylab="P(k)", main="Y2H")
plot(deg.dist.df.y2h, xlab="log k", ylab="log P(k)", main="Y2H", log = "xy", asp)
abline(lm(deg.dist.df.y2h))

Answer 1

You are placing abline on the plot done on log10-log10 scale. Here's one way of doing it
Your code
library("igraph")
tfile<-tempfile()
download.file("http://pdg.cnb.uam.es/pazos/tmp/Yeast_int.txt", tfile)
datosraw <- subset(read.delim(tfile, sep="\t", header=F, stringsAsFactors = F), !is.na(V3) & V3!="" & V3!="METHOD")
names(datosraw)<-c("orf1","orf2","method")
datos<-split(datosraw,datosraw$method)
df.y2h <- graph.data.frame(d = datos$Y2H[1:5125,c(1,2)], directed = FALSE)
The rest can be wrapped in to a helper function
plot_degree_distribution = function(graph) {
# calculate degree
d = degree(graph, mode = "all")
dd = degree.distribution(graph, mode = "all", cumulative = FALSE)
degree = 1:max(d)
probability = dd[-1]
# delete blank values
nonzero.position = which(probability != 0)
probability = probability[nonzero.position]
degree = degree[nonzero.position]
# plot
plot(probability ~ degree, log = "xy", xlab = "Degree (log)", ylab = "Probability (log)",
col = 1, main = "Degree Distribution")
abline(lm(log10(probability) ~ log10(degree)))
}
plot_degree_distribution(df.y2h)