evamaerey / ggpp

Grammar of graphics extensions to 'ggplot2'

ggpp

Purpose

Package ‘ggpp’ provides a set of building blocks that extend the Grammar of Graphics implemented in package ‘ggplot2’ (>= 3.0.0). New geoms support insets in plots, marginal marks and the use of native plot coordinates (npc). Position functions implement new approaches to nudging usable with any geometry, but especially useful together with geom_text_linked(), geom_text_repel() and geom_label_repel().

Extended Grammar of graphics

Geometries

Geometries geom_table(), geom_plot() and geom_grob() make it possible to add inset tables, inset plots, and arbitrary ‘grid’ graphical objects including bitmaps and vector graphics as layers to a ggplot using native coordinates for x and y.

Geometries geom_text_npc(), geom_label_npc(), geom_table_npc(), geom_plot_npc() and geom_grob_npc(), geom_text_npc() and geom_label_npc() are versions of geometries that accept positions on x and y axes using aesthetics npcx and npcy values expressed in “npc” units.

Geometries geom_x_margin_arrow(), geom_y_margin_arrow(), geom_x_margin_grob(), geom_y_margin_grob(), geom_x_margin_point() and geom_y_margin_point() make it possible to add marks along the x and y axes. geom_vhlines() and geom_quadrant_lines() draw vertical and horizontal reference lines within a single layer.

Geometry geom_text_linked() connects text drawn at a nudged position to the original position, usually that of a point being labelled.

Aesthetics and scales

Scales scale_npcx_continuous() and scale_npcy_continuous() and the corresponding new aesthetics npcx and npcy make it possible to add graphic elements and text to plots using coordinates expressed in npc units for the location within the plotting area.

Statistics

Statistic stat_fmt_tb() helps with the formatting of tables to be plotted with geom_table().

Four statistics, stat_dens2d_filter(), stat_dens2d_label(), stat_dens1d_filter() and stat_dens1d_label(), implement tagging or selective labelling of observations based on the local 2D density of observations in a panel. Another two statistics, stat_dens1d_filter_g() and stat_dens1d_filter_g() compute the density by group instead of by plot panel. These six stats are designed to work well together with geom_text_repel() and geom_label_repel() from package ‘ggrepel’.

The statistics stat_apply_panel() and stat_apply_group() can be useful for applying arbitrary functions returning numeric vectors. They are specially useful with functions lime cumsum(), cummax() and diff().

Position functions

New position functions implementing different flavours of nudging are provided: position_nudge_keep(), position_nudge_to(), position_nudge_center() and position_nudge_line(). These last two functions make it possible to apply nudging that varies automatically according to the relative position of points with respect to arbitrary points or lines, or with respect to a polynomial or smoothing spline fitted on-the-fly to the the observations. In contrast to ggplot2::position_nudge() all these functions return the repositioned and original x and y coordinates.

History

This package is a “spin-off” from package ‘ggpmisc’ containing extensions to the grammar originally written for use wihtin ‘ggpmisc’. As ‘ggpmisc’ has grown in size, spliting it into two packages seems the best option. For the time being, package ‘ggpmisc’ will import and re-export visible defintions from ‘ggpp’.

Examples

library(ggpp)
library(ggrepel)
library(dplyr)

A plot with an inset table.

mtcars %>%
  group_by(cyl) %>%
  summarize(wt = mean(wt), mpg = mean(mpg)) %>%
  ungroup() %>%
  mutate(wt = sprintf("%.2f", wt),
         mpg = sprintf("%.1f", mpg)) -> tb

df <- tibble(x = 5.45, y = 34, tb = list(tb))

ggplot(mtcars, aes(wt, mpg, colour = factor(cyl))) +
  geom_point() +
  geom_table(data = df, aes(x = x, y = y, label = tb))

A plot with an inset plot. With the inset plot positioned using native plot coordinates (npc) and using keywords insted of numerical values in the range 0..1 which are also accepted.

p <- ggplot(mtcars, aes(factor(cyl), mpg, colour = factor(cyl))) +
  stat_boxplot() +
  labs(y = NULL, x = "Engine cylinders (number)") +
  theme_bw(9) + theme(legend.position = "none")

ggplot(mtcars, aes(wt, mpg, colour = factor(cyl))) +
  geom_point(show.legend = FALSE) +
  annotate("plot_npc", npcx = "left", npcy = "bottom", label = p) +
  expand_limits(y = 0, x = 0)

Marginal markings

data.tb <- mtcars %>%
  group_by(cyl) %>%
  summarise(wt = mean(wt), mpg = mean(mpg))

ggplot(mtcars, aes(wt, mpg, colour = factor(cyl))) +
  geom_x_margin_arrow(data = data.tb,
                      aes(xintercept = wt, color = factor(cyl)),
                      arrow.length = 0.05) +
  geom_y_margin_arrow(data = data.tb,
                      aes(yintercept = mpg, color = factor(cyl)),
                      arrow.length = 0.05) +
  annotate("plot_npc", npcx = "right", npcy = "top", 
           label = p + theme(axis.title.y = element_blank())) +
  expand_limits(y = 10) +
  geom_point(show.legend = FALSE) 

## Installation

Installation of the most recent stable version from CRAN:

install.packages("ggpp")

Installation of the current unstable version from GitHub:

# install.packages("devtools")
devtools::install_github("aphalo/ggpp")

Documentation

HTML documentation for the package, including help pages and the User Guide, is available at (https://docs.r4photobiology.info/ggpp/).

News about updates are regularly posted at (https://www.r4photobiology.info/).

Chapter 7 in Aphalo (2020) explains both basic concepts of the gramamr of graphics as implemented in ‘ggplot2’ as well as extensions to this grammar including several of those made available by packages ‘ggpp’ and ‘ggpmisc’.

Contributing

Please report bugs and request new features at (https://github.com/aphalo/ggpp/issues). Pull requests are welcome at (https://github.com/aphalo/ggpp).

Citation

If you use this package to produce scientific or commercial publications, please cite according to:

citation("ggpp")

References

Aphalo, Pedro J. (2020) Learn R: As a Language. The R Series. Boca Raton and London: Chapman and Hall/CRC Press. ISBN: 978-0-367-18253-3. 350 pp.

License

© 2016-2021 Pedro J. Aphalo ([email protected]). Released under the GPL, version 2 or greater. This software carries no warranty of any kind.