R packages for semantic similarity measurement

ss-pkg.R

d <- data.frame(pkg = c("GOSim", "GOSemSim", "DOSE", "meshes",
                        "DOSim", "HPOSim", "ppiPre", "MeSHSim", "meshr"),
                year = c(2007, 2010, 2015, 2018, 2011, 2015, 2013, 2015, 2015),
                journal = c("BMC Bioinformatics", rep("Bioinformatics", 3),
                            "BMC Bioinformatics", "PLoS One", "BMC Systems Biology",
                            "Journal of Bioinformatics and computational biology",
                            "BMC Bioinformatics"),
                y = c(1, 1, 2, 3, 2, 4, 5, 2.8, 3.2))

require(ggplot2)

p <- ggplot(d, aes(year, y)) + geom_label(aes(label=paste(pkg, "\n", journal)))  +
    scale_x_continuous(breaks=2007:2018, limits=c(2006.5, 2018.5)) +
    annotate("curve", x=2012, y=5, xend=2010, yend=1.2, colour="steelblue", size=1.2, arrow=arrow(length = unit(0.03, "npc"))) +
    annotate("curve", x=2014.4, y=4, xend=2011, yend=2.2, colour="steelblue", size=1.2, arrow=arrow(length = unit(0.03, "npc"))) +
    annotate("curve", x=2010.1, y=2, xend=2007, yend=1.2, colour="steelblue", size=1.2, arrow=arrow(length = unit(0.03, "npc"))) +
    annotate("text", x=2010, y=4, label="plagiarism", color = "firebrick", size=5, hjust=1) +
    annotate("text", x=2012.5, y=4, label="plagiarism", color = "firebrick", size=5, hjust=1) +
    annotate("text", x=2008.5, y=2.3, label="plagiarism", color = "firebrick", size=5, hjust=1)

p+ ggtree::theme_tree2()