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corrmorant: Flexible Correlation Matrices Based on ggplot2

Roman M. Link

Description

corrmorant extends ggplot2 by an automated framework for plots of correlation matrices that can be easily modified via regular ggplot2 syntax. In addition, it provides a large set of visualization tools for exploratory data analysis based on correlation matrices.

Update 2020-07-07: As of today, the corrmorant package will replace all uses of the iris dataset with the drosera dataset, which contains a set of (eugenics-free) biometric measurements of three African sundew species and is available as a separate data-package.

Update 2020-04-28: So far, the package seems to work fine with R. v. 4.0.0. Keep me informed if you notice any unwanted behavior.

Update 2020-03-06: The package passes all tests with the newest ggplot2version (v. 3.3.0), but I haven’t been able to check more thoroughly. I you notice any strange behavior with the new version, please let me know!

A big thank you goes out to the developers of the software without which this package would not be possible, especially Hadley Wickham and the rest of the ggplot2 development team for their incredible work.

Installation

The package can be installed from Github using remotes::install_github():

# install remotes package if necessary
install.packages("remotes")
# install corrmorant from the github repository
remotes::install_github("r-link/corrmorant")

Afterwards, the package can be loaded regularly via library():

library(corrmorant)

Simple plots with corrmorant()

The corrmorant() function is a simple wrapper function around the more complex gcorrm() function that can be used to create first, simple plots of correlation matrices for initial data inspection. Currently, three different styles are available, “light”, “dark” and the default, “blue_red”:

# correlation plot of the drosera data using style = 'light'
corrmorant(drosera, style = "light")
# the "dark" style has a dark background in the diagonal facets
corrmorant(drosera, style = "dark")
# in the "blue_red" style, colors and correlation labels are colored by the strength of
# correlation
corrmorant(drosera, style = "blue_red")

It obvious that this illustration is not optimal because the three different Drosera species have remarkably different leaf morphologies. More complex plots (e.g. with different correlations for different groups) are possible with ggcorrm().

Basic usage of ggcorrm()

While corrmorant() may be useful for many basic data inspection tasks, its functionality is rather limited. If you want to take control of the elements in a plot, you can use ggcorrm() together with the corrmorant selector functions lotri(), utri() and dia() that direct ggplot layers to the lower or upper triangle or the plot diagonal of a ggcorrm() plot, respectively. In addition, corrmorant offers a series of utility functions for readymade data summaries on the plot diagonal (dia_names(), dia_density(), dia_histogram and dia_freqpoly()) as well as a couple of new stats, e.g. stat_corrtext() for displaying correlation strength in correlation plot facets. The new corrmorant stats can generally be called in a simplified form by prefixing their name with lotri_ or utri_, e.g. lotri_corrtext() and utri_corrtext()

For example, corrmorant(drosera, style = "light") can be recreated by the following code:

p1 <- ggcorrm(drosera) +
  lotri(geom_point(alpha = 0.5)) +
  utri_corrtext() +
  dia_names(y_pos = 0.15, size = 3) +
  dia_density(lower = 0.3, fill = "grey80", color = 1)
p1

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If you want, you can add additional ggplot2 layers, using the appropriate corrmorant selectors to restrict them to the appropriate set of facets. For example, you might want to display a linear trend in the facets on the lower triangle:

p1 + lotri(geom_smooth(method = "lm"))

## `geom_smooth()` using formula 'y ~ x'

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The horrific fit of these linear regressions results from the fact that the drosera dataset contains data from three different sundew species. You might want to include this information into your plot by plotting the three species in different colours, which can easily be achieved by setting plot level aesthetics using the mapping argument of ggcorrm():

ggcorrm(drosera, mapping = aes(col = species, fill = species)) +
  lotri(geom_smooth(method = "lm")) +
  lotri(geom_point(alpha = 0.5)) +
  utri_corrtext(nrow = 2, squeeze = 0.6) +
  dia_names(y_pos = 0.15, size = 3) +
  dia_density(lower = 0.3, color = 1)

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Special corrmorant stats and geoms

Coloring data by correlation strength

To color a dataset by correlation strength, you can use the .corr column internally created in tidy_corrm() together with scale_colour_corr() or scale_fill_corr():

# simulate some data from a multivariate normal distribution
# (mtcars is only used as a shortcut to a positive definite covariance matrix)
data1 <- MASS::mvrnorm(100, colMeans(mtcars),  cov(mtcars))[, 1:8]
colnames(data1) <- paste("Var.", 1:ncol(data1))

# create plot
ggcorrm(data1, 
        mapping = aes(col = .corr, fill = .corr),
        bg_dia = "grey20", 
        rescale = "by_sd") +
  lotri(geom_smooth(method = "lm", size = .3)) +
  lotri(geom_point(alpha = 0.5)) +
  utri_corrtext(nrow = 2, squeeze = 0.6) +
  dia_names(y_pos = 0.15, size = 3, color = "white") +
  dia_histogram(lower = 0.3, color = "grey80", fill = "grey60", size = .3) +
  scale_color_corr(aesthetics = c("fill", "color"))

## `geom_smooth()` using formula 'y ~ x'

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Correlation heatmaps and more

corrmorant offers a series of new geoms and stats that are designed to improve the display of correlation strength.

For example, there is a set of stats for correlation heatmaps and the likes, which can be useful when inspecting datasets with large numbers of variables:

select(mtcars, mpg, disp:qsec) %>% 
ggcorrm(rescale = "by_sd") +
  utri_heatmap(alpha = 0.5) +
  lotri_heatcircle(alpha = 0.5, col = 1) +
  utri_corrtext() +
  dia_names(y_pos = 0.15, size = 3) +
  dia_density(lower = 0.3, fill = "lightgrey", color = 1) +
  scale_fill_corr() 

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With lotri_/utri_heatpoint(), you can scale the diameter of any character you want by correlation strength. And yes, you’re right, this means you can display correlation strength by the size of purple skulls and angry cat faces (at least if your graphical device allows Unicode characters, which might or might not work on Windows):

airquality %>% 
ggcorrm() +
  lotri_heatpoint(pch = "\U1F63E") +
  utri_heatpoint(pch = "\U2620", col = "#660066") +
  dia_names(y_pos = 0.15, size = 3) +
  dia_density(lower = 0.3, fill = "#89DFA3", color = 1) +
  scale_size(range = c(1, 15)) + 
  scale_color_corr(option = "C")

## Some variables are highly skewed (abs(skew) > 1).
## Consider transformation for better display.

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Print output of arbitrary functions of the data

If you want to place text labels for the output of arbitrary functions in your plots, you can use lotri/utri_funtext(), which uses the same placement rules as stat_corrtext().

For instance, you could add labels for the slope of the linear models in the lower triangle (note how y and x are swapped to account for the reverse axes in the upper triangle).

# function to compute linear model slopes
lmslope <- function(x, y)  round(coef(lm(x ~ y))[2], 2)

# add slopes using a function
ggcorrm(drosera, mapping = aes(col = species, fill = species)) +
  lotri(geom_point(alpha = 0.4)) +
  lotri(geom_smooth(alpha = 0.4, method = "lm")) +
  utri_funtext(fun = lmslope, squeeze = 0.6) +
  dia_density(lower = 0.3, col = 1, alpha = 0.4) +
  dia_names(y_pos = 0.15)

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Besides using a two-parameter formula, stat_funtext(), the stat underlying lotri/utri_funtext(), also accepts rlang style lambda expressions describing functions and quosures generated with quo() (referring to the variable names x and y).

Here are two ways to copy the output of stat_corrtext() - using a lambda expression (a formula containing .x and .y) in the upper and a quosure in the lower triangle:

ggcorrm(drosera, aes(col = .corr), rescale = "as_is") +
  utri_funtext(fun = ~ round(cor(.x, .y), 2)) +
  lotri_funtext(fun = quo(round(cor(x, y), 2))) +
  dia_names(y_pos = 0.5) +
  scale_color_corr()

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