Package {BoxDensityPlot}

Type: Package
Title: Multi-Trait Density and Boxplot Visualization
Version: 0.1.0
Description: Reads wide-format phenotypic data (one row per genotype or sample, one column per trait) from CSV or 'Excel' files, reshapes it to long format, and produces faceted figures that combine a mirrored density curve with a boxplot for each trait. Density curves can be drawn on the left, right, or both sides of the box, and figures can be saved automatically at publication resolution.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (≥ 4.1.0)
Imports: ggplot2 (≥ 3.4.0), dplyr (≥ 1.1.0), tidyr (≥ 1.3.0), rlang, readxl, stats, utils, grid, tools
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
RoxygenNote: 7.3.1
NeedsCompilation: no
Packaged: 2026-09-28 11:44:21 UTC; iasri
Author: Prakash Kumar [aut, cre], Himadri Sekhar Roy [aut], Ranjit Kumar Paul [aut], Md. Yeasin [aut], Paritosh Kumar ICAR-NIASM [aut], Amrit Kumar Paul [aut]
Maintainer: Prakash Kumar <prakash289111@gmail.com>
Repository: CRAN
Date/Publication: 2026-10-08 10:40:26 UTC

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)

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.

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

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)