Here is the graph, drawn with ggplot:
You will need to download the data to use it. This can be done from here. Then I went into Excel and saved it as a csv file. This script imports the file and produces the graph.
setwd("/Users/... ") # point this to where the file is...
##Identify the genes that have a p-value < 0.05
data$threshold = as.factor(data$P.Value < 0.05)
##Construct the plot object
g <- ggplot(data=data,
aes(x=Log2.Fold.Change, y =-log10(P.Value),
geom_point(alpha=0.4, size=1.75) +
xlim(c(-6, 6)) +
xlab("log2 fold change") + ylab("-log10 p-value") +
# The script gives a warning message: Removed 1 rows containing missing values (geom_point).
# but it still works....
These pages helped me write this script: