Package 'BoxDensityPlot'

Path to the bundled example trait data set

Description

Returns the file path to a small example CSV bundled with the package, containing genotype-level values for six traits. Useful for examples, tests, and trying out plot_trait_density_box.

Usage

example_trait_data()

Value

A file path (character string).

Examples

f <- example_trait_data()
dat <- read_trait_data(f)
head(dat)

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Build a density + boxplot figure for multiple traits

Description

Creates a faceted ggplot2 figure that overlays a mirrored density curve (violin-style) with a boxplot for each trait found in long_data. This is the low-level plot builder used internally by plot_trait_density_box; call it directly if you already have data prepared in the expected long format.

Usage

make_density_boxplot(
  long_data,
  density_data,
  ncol_plot,
  density_position = c("both", "left", "right"),
  density_colour = "#4DBBD5",
  plot_title = NULL,
  density_width = 0.45,
  density_alpha = 0.3,
  boxplot_width = 0.25,
  box_colour = "#006D6F",
  mean_colour = "#E31A1C"
)

Arguments

long_data	Long-format data frame with (at least) columns Trait and Value.
density_data	Long-format data frame with columns Trait, Value, and Density_scaled, one row per point on each trait's estimated density curve.
ncol_plot	Number of facet columns.
density_position	One of "both", "left", or "right": which side(s) of the boxplot show the density curve.
density_colour	Fill colour for the density ribbon.
plot_title	Title shown above the figure. Use NULL for no title.
density_width	Numeric half-width of the density curve.
density_alpha	Fill transparency (0-1) of the density ribbon.
boxplot_width	Numeric width of the boxplot.
box_colour	Fill colour of the boxplot.
mean_colour	Fill colour of the mean point marker.

Value

A ggplot object.

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Read trait data and generate density + boxplot figure(s)

Description

High-level, one-call wrapper that reads a wide-format CSV or Excel file of multi-trait data (one row per genotype/sample, one column per trait), reshapes it, builds one or more density + boxplot figures (see make_density_boxplot), and optionally saves each one to disk at publication resolution.

Usage

plot_trait_density_box(
  file,
  genotype_col = "Genotype",
  density_position = c("both", "left", "right"),
  save = FALSE,
  out_dir = NULL,
  prefix = "Multiple_Traits_Boxplot_Density",
  format = "jpg",
  dpi = 600,
  width = NULL,
  height = NULL,
  ...
)

Arguments

file	Path to a .csv, .xls, or .xlsx file, or a data frame already in wide format (one identifier column plus one column per trait).
genotype_col	Name of the identifier column (e.g. "Genotype").
density_position	Which figure(s) to build: any combination of "both", "left", "right". Defaults to all three.
save	Logical; if TRUE each figure is saved with ggsave.
out_dir	Directory to save figures into. Must be supplied explicitly when save = TRUE; no output directory is assumed by default.
prefix	File name prefix for saved figures.
format	Image format passed to ggsave (e.g. "jpg", "png", "pdf", "tiff").
dpi	Resolution (dots per inch) for saved figures.
width, height	Figure size in inches. If NULL (default) a size is chosen automatically from the number of traits, matching the original script's behaviour.
...	Additional styling arguments forwarded to make_density_boxplot: density_width, density_alpha, boxplot_width, box_colour, mean_colour, plus the per-position ribbon colours both_colour, left_colour, right_colour.

Value

A named list of ggplot objects (one per requested density_position), returned invisibly.

Examples

f <- example_trait_data()
plots <- plot_trait_density_box(f, save = FALSE)
plots$both

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Read multi-trait phenotypic data from CSV or Excel

Description

Reads a wide-format data set (one row per genotype/sample, one column per trait) from a .csv, .xls, or .xlsx file.

Usage

read_trait_data(file, sheet = 1, genotype_col = "Genotype")

Arguments

file	Path to the input file. The file extension (.csv, .xls, .xlsx) determines how the file is parsed.
sheet	Sheet name or index to read when file is an Excel file. Ignored for CSV files. Defaults to the first sheet.
genotype_col	Name of the identifier column (genotype, sample, accession, etc.). Defaults to "Genotype".

Value

A data frame in wide format with the identifier column plus one column per trait.

Examples

f <- example_trait_data()
dat <- read_trait_data(f)
head(dat)

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