xplot_box: Default xpose box plot function

In Certara.Xpose.NLME: Enhances 'xpose' Diagnostics for Pharmacometric Models from 'Certara.RsNLME' and Phoenix NLME

Default xpose box plot function

Description

Manually generate categorical covariate box plots against eta.

Usage

xplot_box(
  xpdb,
  mapping = NULL,
  type = "b",
  guide = FALSE,
  yscale = "continuous",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  tag = NULL,
  plot_name = "box_plot",
  gg_theme,
  xp_theme,
  opt,
  quiet,
  ...
)

Arguments

xpdb	An xpose database object.
mapping	List of aesthetics mappings to be used for the xpose plot (e.g. point_color).
type	String setting the type of plot to be used. Only 'b' applicable.
guide	Enable guide display (e.g. unity line).
yscale	Scale type for y axis (e.g. 'continuous', 'discrete', 'log10').
title	Plot title. Use NULL to remove.
subtitle	Plot subtitle. Use NULL to remove.
caption	Page caption. Use NULL to remove.
tag	Plot identification tag. Use NULL to remove.
plot_name	Name to be used by xpose::xpose_save() when saving the plot.
gg_theme	A complete ggplot2 theme object (e.g. ggplot2::theme_classic), a function returning a complete ggplot2 theme, or a change to the current gg_theme.
xp_theme	A complete xpose theme object (e.g. theme_xp_default) or a list of modifications to the current xp_theme (e.g. list(point_color = 'red', line_linetype = 'dashed')).
opt	A list of options in order to create appropriate data input for ggplot2. For more information see data_opt.
quiet	Logical, if FALSE messages are printed to the console.
...	Any additional aesthetics to be passed on xplot_scatter.

Value

An object of class xpose_plot, ggplot, and gg. This object represents a customized plot created using ggplot2. The xpose_plot class provides additional metadata and integration with xpose workflows, allowing for advanced customization and compatibility with other xpose functions. Users can interact with the plot object as they would with any ggplot2 object, including modifying aesthetics, adding layers, or saving the plot.

Faceting

Every xpose plot function has built-in faceting functionalities. Faceting arguments are passed to the functions facet_wrap_paginate when the facets argument is a character string (e.g. facets = c('SEX', 'MED1')) or facet_grid_paginate when facets is a formula (e.g. facets = SEX~MED1). All xpose plot functions accept all the arguments for the facet_wrap_paginate and facet_grid_paginate functions e.g. dv_vs_ipred(xpdb_ex_pk, facets = SEX~MED1, ncol = 3, nrow = 3, page = 1, margins = TRUE, labeller = 'label_both').

Faceting options can either be defined in plot functions (e.g. dv_vs_ipred(xpdb_ex_pk, facets = 'SEX')) or assigned globally to an xpdb object via the xp_theme (e.g. xpdb <- update_themes(xpdb_ex_pk, xp_theme = list(facets = 'SEX'))). In the latter example all plots generate from this xpdb will automatically be stratified by 'SEX'.

By default, some plot functions use a custom stratifying variable named 'variable', e.g. eta_distrib(). When using the facets argument, 'variable' needs to be added manually e.g. facets = c('SEX', 'variable') or facets = c('SEX', 'variable'), but is optional, when using the facets argument in xp_theme variable is automatically added whenever needed.

Layers mapping

Plots can be customized by mapping arguments to specific layers. The naming convention is layer_option where layer is one of the names defined in the list below and option is any option supported by this layer e.g. boxplot_fill = 'blue', etc.

• box plot: options to geom_boxplot

• yscale: options to scale_y_continuous or scale_y_log10

See Also

xplot_scatter xplot_qq

Examples

# Categorical Covariate MED1 vs ETA1
xplot_box(xpose::xpdb_ex_pk, ggplot2::aes(x = MED1, y = ETA1))

# Categorical Covariate SEX vs CL
xplot_box(xpose::xpdb_ex_pk, ggplot2::aes(x = SEX, y = CL))

Certara.Xpose.NLME documentation built on April 3, 2025, 7:45 p.m.