Format taxonomic names for italic display in ggplot2

Converts taxonomic names in one or more columns to plotmath italic expressions suitable for use in ggplot2 axis labels or legends via ggplot2::label_parsed. A new column named <column>_italic is appended to the data frame for each input column.

Usage

italicize(data, columns, drop_na = FALSE)

Arguments

data

A data frame.

columns

Column name or c() of column names to italicize, supplied either unquoted (SciName) or quoted ("SciName"). Each named column must contain character strings (e.g. "Homo sapiens").

drop_na

Logical. If TRUE, rows with NA in any of the specified columns are dropped before conversion. Default is FALSE.

Value

The input data frame with one additional character column appended per entry in columns, named <column>_italic. Each new column contains a plotmath expression of the form "italic(Genus~species)", where spaces are replaced with ~ to preserve word spacing when rendered. NA values in the source column remain NA in the output column when drop_na = FALSE.

Details

The _italic columns are intended to be mapped to a ggplot2 aesthetic (e.g. aes(x = Species_italic)) and rendered as parsed expressions by passing label_parsed to the labels argument of the corresponding scale. This keeps names as plain character data until the plot is rendered, avoiding manual expression() calls.

Authorship strings appended by taxon_cite in the format "Genus species (Author, Year)" are automatically detected and rendered in roman type alongside the italic canonical name, producing expressions of the form italic("Genus species")~"(Author, Year)".

Spaces in names are replaced with ~ prior to wrapping in italic(), which is required for plotmath to render multi-word names (e.g. genus + species) correctly.

See also

taxon_cleaner for standardising taxonomic name formatting before italicising,

taxon_combine for merging genus and epithet into a binomial name before italicising,

taxon_validate for validating taxonomic names before italicising,

taxon_spellcheck for correcting misspellings before italicising,

taxon_cite for appending authorship in the format detected and rendered by this function,

label_parsed for rendering plotmath expressions in ggplot2 scales.

Examples

df <- data.frame(
  SciName = c("Homo sapiens", "Panthera leo", "Canis lupus"),
  count   = c(120, 45, 78)
)

# Italicize a single column
df <- italicize(df, SciName)
df$SciName_italic
#> [1] "italic(\"Homo sapiens\")" "italic(\"Panthera leo\")"
#> [3] "italic(\"Canis lupus\")" 

# Use in a ggplot2 axis with parsed labels
# \donttest{
if (requireNamespace("ggplot2", quietly = TRUE)) {
  ggplot2::ggplot(df, ggplot2::aes(x = SciName_italic, y = count)) +
    ggplot2::geom_col() +
    ggplot2::scale_x_discrete(labels = ggplot2::label_parsed)
}

# }

# Italicize multiple columns at once
df2 <- data.frame(
  genus   = c("Homo", "Panthera"),
  species = c("sapiens", "leo")
)
italicize(df2, c(genus, species))
#>      genus species       genus_italic    species_italic
#> 1     Homo sapiens     italic("Homo") italic("sapiens")
#> 2 Panthera     leo italic("Panthera")     italic("leo")

# Drop rows where the name column is NA
df_na <- data.frame(
  SciName = c("Homo sapiens", NA, "Canis lupus"),
  count   = c(10, 5, 8)
)
italicize(df_na, SciName, drop_na = TRUE)
#>        SciName count         SciName_italic
#> 1 Homo sapiens    10 italic("Homo sapiens")
#> 3  Canis lupus     8  italic("Canis lupus")