The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

ggpointdensity

Introduces geom_pointdensity(): A cross between a scatter plot and a 2D density plot.

Installation

To install the package from R, use:

install.packages("ggpointdensity")

Alternatively, you can install the development version from GitHub:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("LKremer/ggpointdensity")

Motivation

There are several ways to visualize data points on a 2D coordinate system: If you have lots of data points on top of each other, geom_point() fails to give you an estimate of how many points are overlapping. geom_density2d() and geom_bin2d() solve this issue, but they make it impossible to investigate individual outlier points, which may be of interest.

geom_pointdensity() aims to solve this problem by combining the best of both worlds: individual points are colored by the number of neighboring points. This allows you to see the overall distribution, as well as individual points.

Demo

Generate some toy data and visualize it with geom_pointdensity():

library(ggplot2)
library(dplyr)
library(viridis)
library(ggpointdensity)

dat <- bind_rows(
  tibble(x = rnorm(7000, sd = 1),
         y = rnorm(7000, sd = 10),
         group = "foo"),
  tibble(x = rnorm(3000, mean = 1, sd = .5),
         y = rnorm(3000, mean = 7, sd = 5),
         group = "bar"))

ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity() +
  scale_color_viridis()

Each point is colored according to the number of neighboring points. The distance threshold to consider two points as neighbors (smoothing bandwidth) can be adjusted with the adjust argument, where adjust = 0.5 means use half of the default bandwidth.

ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity(adjust = .1) +
  scale_color_viridis()
 
ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity(adjust = 4) +
  scale_color_viridis()

Of course you can combine the geom with standard ggplot2 features such as facets…

# Facetting by group
ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity() +
  scale_color_viridis() +
  facet_wrap( ~ group)

… or point shape and size:

dat_subset <- sample_frac(dat, .1)  # smaller data set
ggplot(data = dat_subset, mapping = aes(x = x, y = y)) +
  geom_pointdensity(size = 3, shape = 17) +
  scale_color_viridis()

Zooming into the axis works as well, keep in mind that xlim() and ylim() change the density since they remove data points. It may be better to use coord_cartesian() instead.

ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity() +
  scale_color_viridis() +
  xlim(c(-1, 3)) + ylim(c(-5, 15))

ggplot(data = dat, mapping = aes(x = x, y = y)) +
  geom_pointdensity() +
  scale_color_viridis() +
  coord_cartesian(xlim = c(-1, 3), ylim = c(-5, 15))

Authors

Lukas Kremer and Simon Anders (2019)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.