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Plot Publications Citing DO by Year

plot_citedby.Rd

Plots the count of publications that cite the Human Disease Ontology by year.

Usage

plot_citedby(
  data_file = "data/citedby/DO_citedby.csv",
  out_dir = "graphics/website",
  color_set = c(Article = "#4C3E45", `Clinical Trial` = "#B9964B", Book = "#83C85F",
    Conference = "#95B1BB", Review = "#934FBB", Other = "#C45055", Retracted = "#000000"),
  retracted = "warn",
  w = 6,
  h = 3.15
)

Arguments

data_file

The path to the file containing the list of publications citing the DO, as a string.

out_dir

The directory where the plot "DO_cited_by_count.png" should be saved, as a string. If NULL the plot is not saved to disk.

color_set

A named set of 7 colors, one for each of the possible publication types (see Colors section) or the prefix of the color set to use from DO_colors, as a character vector.

retracted

How to handle retracted publications, as a string. One of:

  • "warn" (default) to drop them with a warning.

  • "include" to display them in the plot in their own category.

  • "other" to include them in the "Other" category.

w

The width of the plot in inches, as numeric.

h

The height of the plot in inches, as numeric.

Data Preparation

To prepare data, execute scripts/citedby_full_procedure.R.

Colors

If specifying a color set manually, one color should be included for each of the following publication types: "Article", "Book", "Clinical Trial", "Conference", "Review", "Other", "Retracted". "Other" serves as a catch all category (generally a small subset of otherwise uncategorized publications).

Sets available in DO_colors include: "sat" (saturated), "accent1", "accent2", and "orange". The default and light versions of the specified color set will be used to generate a gradient.