ggcognigen

ggcognigen provides geoms, themes, styles, and helper functions for {ggplot2} at the Clinical Pharmacology and Pharmacometrics (CPP) business unit of Simulations Plus, Inc.

Load it with:

library(ggcognigen)

Functionality

Themes

CPP themes are based on ggplot2::theme_bw(). Additional theme() inputs can be passed to ... for further customization.

• theme_cognigen(): simple theme for CPP plots (without grid lines).
• theme_cognigen_grid(): similar to theme_cognigen() but displaying grid lines in the background.

Geoms

Additional geom functions:

• geom_barcount(): a utility function working in combination with geom_bar() and allowing the display of the (possibly cumulative) count, normalized count, or percentages of the data represented by each bar.
• geom_boxplot2(): a variant on ggplot2::geom_boxplot() allowing users to set whisker limits based upon a confidence interval rather than a multiple of the IQR, display outliers with jitter, and providing a slightly different graphical styles for grouping/coloring.
• geom_boxcount(): a utility function working in combination with geom_boxplot2() allowing the display of the number of data points used for the calculation of statistics which are graphically represented by each box and whiskers.
• geom_histcount(): a utility function working in combination with geom_histogram() and allowing the display of the cumulative count, density, or percentage of data in each histogram bar.

Stats

Additional stat functions:

• stat_barcount(): associated with geom_barcount.
• stat_bin2(): a variant of ggplot2::bin() which exports the percent variable in addition to the default count and density variables. Mostly intended to be used with ggplot2::geom_histogram() and stat_histcount() when percentages are required.
• stat_count2(): a variant of ggplot2::count() which exports the percent variable in addition to the default count and prop variables. Mostly intended to be used with ggplot2::geom_bar() and stat_barcount() when percentages are required.
• stat_boxplot2(): a variant of ggplot2::stat_boxplot() which supports geom_boxplot2().
• stat_boxcount(): associated with geom_boxcount().
• stat_histcount(): associated with geom_histcount().

Positions

New position function:

• position_fillpercent(): a variant of ggplot2::position_fill() which normalizes the data to 100 instead of 1. Mostly intended for use with ggplot2::geom_bar() and geom_barcount() for display of data in percentages.

Style and scale functions for mapping aesthetics

These control aesthetics that are mapped to data such as color, fill, linetype, shape, and size.

• cognigen_style()
• scale_discrete_cognigen()
• set_default_style()
• read_style()

Forest plots

Additional functions for creation of forest plots:

• make_gmr_data(): a function to calculate and report geometric means (GM) and geometric mean ratios (GMR).
• make_gmr_table(): a function to format and write GMR table (typically created by make_gmr_data()) to html, docx, or tex files.
• make_forestplot(): a function to create a forest plot as a ggplot2 object and based upon the GRM table created by make_gmr_data().

Miscellaneous helper functions

• ggsave_multiple(): extension of ggplot2::ggsave to save multiple plots and multi-page plots like those created using ggforce::facet_grid_paginate() or ggforce::facet_wrap_paginate().
• get_device_size(): a utility function returning default device dimensions based upon a number of plots/panels per page.
• format_continuous_cognigen(): a utility function be passed to the labels argument of a scale_ function in order to automatically format axis ticks numerical labels in default or scientific notation (beyond pre-defined value limits)