Plotting degree distribution with igraph and ggplot2

ak.degree.distro.r

# Anton Kratz
# date: Sat Jul 21 17:03:22 PDT 2018
suppressPackageStartupMessages(library("igraph"))
suppressPackageStartupMessages(library("ggplot2"))

# Load the PG Yeast Net file - two large components and many small ones 
rf <- read.table("~/git/assets/INT.PG.YeastNet.v3.2463gene.54496link.txt", sep="\t")
akg <- graph_from_data_frame(rf, directed = FALSE, vertices = NULL)

# List of degrees
d <- degree(akg)

# Let's count the frequencies of each degree
d.histogram <- as.data.frame(table(d))

# Need to convert the first column to numbers, otherwise
# the log-log thing will not work (that's fair...)
d.histogram[,1] <- as.numeric(d.histogram[,1])

# Now, plot it!
ggplot(d.histogram, aes(x = d, y = Freq)) +
  geom_point() +
  scale_x_continuous("Degree\n(nodes with this amount of connections)",
                     breaks = c(1, 3, 10, 30, 100, 300),
                     trans = "log10") +
  scale_y_continuous("Frequency\n(how many of them)",
                     breaks = c(1, 3, 10, 30, 100, 300, 1000),
                     trans = "log10") +
  ggtitle("Degree Distribution (log-log)")
ggsave("degree.png")