The function ggstatsplot::ggcorrmat provides a quick way to produce publication-ready correlation matrix (aka correlalogram) plot. The function can also be used for quick data exploration. In addition to the plot, it can also be used to get a correlation coefficient matrix or the associated p-value matrix. Currently, the plot can display Pearson’s r, Spearman’s rho, and Kendall’s tau, and robust correlation coefficient (percentage bend correlation; see ?WRS2::pbcor). This function is a convenient wrapper around ggcorrplot::ggcorrplot function with some additional functionality.

We will see examples of how to use this function in this vignette with the gapminder and diamonds dataset.

To begin with, here are some instances where you would want to use ggcorrmat-

to easily visualize a correlation matrix using ggplot2
to quickly explore correlation between (all) numeric variables in the dataset

Note before: The following demo uses the pipe operator (%>%), so in case you are not familiar with this operator, here is a good explanation: http://r4ds.had.co.nz/pipes.html

Correlation matrix plot with `ggcorrmat`

For the first example, we will use the gapminder dataset (available in eponymous package on CRAN) provides values for life expectancy, Gross Domestic Product (GDP) per capita, and population, every five years, from 1952 to 2007, for each of 142 countries and was collected by the Gapminder Foundation. Let’s have a look at the data-

library(gapminder)
library(dplyr)

dplyr::glimpse(gapminder)
#> Rows: 1,704
#> Columns: 6
#> $ country   <fct> Afghanistan, Afghanistan, Afghanistan, Afghanistan, Afgha...
#> $ continent <fct> Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asia, Asi...
#> $ year      <int> 1952, 1957, 1962, 1967, 1972, 1977, 1982, 1987, 1992, 199...
#> $ lifeExp   <dbl> 28.801, 30.332, 31.997, 34.020, 36.088, 38.438, 39.854, 4...
#> $ pop       <int> 8425333, 9240934, 10267083, 11537966, 13079460, 14880372,...
#> $ gdpPercap <dbl> 779.4453, 820.8530, 853.1007, 836.1971, 739.9811, 786.113...

Let’s say we are interested in studying correlation between population of a country, average life expectancy, and GDP per capita across countries only for the year 2007.

The simplest way to get a correlation matrix is to stick to the defaults-

# setup
set.seed(123)
library(ggstatsplot)

# select data only from the year 2007
gapminder_2007 <- dplyr::filter(.data = gapminder::gapminder, year == 2007)

# producing the correlation matrix
ggstatsplot::ggcorrmat(
  data = gapminder_2007, # data from which variable is to be taken
  cor.vars = lifeExp:gdpPercap # specifying correlation matrix variables
)

This plot can be further modified with additional arguments-

ggstatsplot::ggcorrmat(
  data = gapminder_2007, # data from which variable is to be taken
  cor.vars = lifeExp:gdpPercap, # specifying correlation matrix variables
  cor.vars.names = c(
    "Life Expectancy",
    "population",
    "GDP (per capita)"
  ),
  type = "spearman", # which correlation coefficient is to be computed
  lab.col = "red", # label color
  ggtheme = ggplot2::theme_light(), # selected ggplot2 theme
  ggstatsplot.layer = FALSE, # turn off default ggestatsplot theme overlay
  matrix.type = "lower", # correlation matrix structure
  colors = NULL, # turning off manual specification of colors
  palette = "category10_d3", # choosing a color palette
  package = "ggsci", # package to which color palette belongs
  title = "Gapminder correlation matrix", # custom title
  subtitle = "Source: Gapminder Foundation" # custom subtitle
)

As seen from this correlation matrix, although there is no relationship between population and life expectancy worldwide, at least in 2007, there is a strong positive relationship between GDP, a well-established indicator of a country’s economic performance.

Given that there were only three variables, this doesn’t look that impressive. So let’s work with another example from ggplot2 package: the diamonds dataset. This dataset contains the prices and other attributes of almost 54,000 diamonds.

Let’s have a look at the data-

library(ggplot2)

dplyr::glimpse(ggplot2::diamonds)
#> Rows: 53,940
#> Columns: 10
#> $ carat   <dbl> 0.23, 0.21, 0.23, 0.29, 0.31, 0.24, 0.24, 0.26, 0.22, 0.23,...
#> $ cut     <ord> Ideal, Premium, Good, Premium, Good, Very Good, Very Good, ...
#> $ color   <ord> E, E, E, I, J, J, I, H, E, H, J, J, F, J, E, E, I, J, J, J,...
#> $ clarity <ord> SI2, SI1, VS1, VS2, SI2, VVS2, VVS1, SI1, VS2, VS1, SI1, VS...
#> $ depth   <dbl> 61.5, 59.8, 56.9, 62.4, 63.3, 62.8, 62.3, 61.9, 65.1, 59.4,...
#> $ table   <dbl> 55, 61, 65, 58, 58, 57, 57, 55, 61, 61, 55, 56, 61, 54, 62,...
#> $ price   <int> 326, 326, 327, 334, 335, 336, 336, 337, 337, 338, 339, 340,...
#> $ x       <dbl> 3.95, 3.89, 4.05, 4.20, 4.34, 3.94, 3.95, 4.07, 3.87, 4.00,...
#> $ y       <dbl> 3.98, 3.84, 4.07, 4.23, 4.35, 3.96, 3.98, 4.11, 3.78, 4.05,...
#> $ z       <dbl> 2.43, 2.31, 2.31, 2.63, 2.75, 2.48, 2.47, 2.53, 2.49, 2.39,...

Let’s see the correlation matrix between different attributes of the diamond and the price.

# for reproducibility
set.seed(123)

# let's use just 5% of the data to speed it up
ggstatsplot::ggcorrmat(
  data = dplyr::sample_frac(tbl = ggplot2::diamonds, size = 0.05),
  cor.vars = c(carat, depth:z), # note how the variables are getting selected
  cor.vars.names = c(
    "carat",
    "total depth",
    "table",
    "price",
    "length (in mm)",
    "width (in mm)",
    "depth (in mm)"
  ),
  ggcorrplot.args = list(outline.color = "black", hc.order = TRUE)
)

We can make a number of changes to this basic correlation matrix. For example, since we were interested in relationship between price and other attributes, let’s make the price column to the the first column. Additionally, since we are running 6 correlations that are of a priori interest to us, we can adjust our threshold of significance to (0.05/6 ~ 0.008). Additionally, let’s use a non-parametric correlation coefficient. Please note that it is important to always make sure that the order in which cor.vars and cor.vars.names are entered is in sync. Otherwise, wrong column labels will be displayed.

# for reproducibility
set.seed(123)

# let's use just 5% of the data to speed it up
ggstatsplot::ggcorrmat(
  data = dplyr::sample_frac(tbl = ggplot2::diamonds, size = 0.05),
  cor.vars = c(price, carat, depth:table, x:z), # note how the variables are getting selected
  cor.vars.names = c(
    "price",
    "carat",
    "total depth",
    "table",
    "length (in mm)",
    "width (in mm)",
    "depth (in mm)"
  ),
  type = "spearman",
  matrix.type = "lower",
  title = "Relationship between diamond attributes and price",
  subtitle = "Dataset: Diamonds from ggplot2 package",
  colors = c("#0072B2", "#D55E00", "#CC79A7"),
  pch = "square cross",
  # additional aesthetic arguments passed to `ggcorrmat`
  ggcorrplot.args = list(
    lab_col = "yellow",
    lab_size = 6,
    tl.srt = 90,
    pch.col = "white",
    pch.cex = 14
  ),
  caption =
    substitute(
      paste(italic("Note"), ": Point shape denotes correlation non-significant at p < 0.008; adjusted for 6 comparisons")
    )
) + # modification outside ggstatsplot using ggplot functions
  ggplot2::theme(
    axis.text.x = ggplot2::element_text(
      margin = ggplot2::margin(t = 0.15, r = 0.15, b = 0.15, l = 0.15, unit = "cm")
    )
  )

As seen here, and unsurprisingly, the strongest predictor of the diamond price is its carat value, which a unit of mass equal to 200 mg. In other words, the heavier the diamond, the more expensive it is going to be.

Dataframe containing statistics with `ggcorrmat`

Another utility of ggcorrmat is in obtaining a dataframe containing all details from statistical analyses. Such dataframes can be easily embedded in manuscripts as tables.

# for reproducibility
set.seed(123)

# to get correlations
ggstatsplot::ggcorrmat(
  data = dplyr::sample_frac(tbl = ggplot2::txhousing, size = 0.15),
  cor.vars = sales:inventory,
  output = "dataframe",
  type = "robust",
  digits = 3
)
#> # A tibble: 10 x 10
#>    parameter1 parameter2      r ci_low ci_high      t    df        p method
#>    <chr>      <chr>       <dbl>  <dbl>   <dbl>  <dbl> <dbl>    <dbl> <chr> 
#>  1 sales      volume      0.980  0.978   0.982 172.    1202 0.       Perce~
#>  2 sales      median      0.469  0.423   0.512  18.3   1195 0.       Perce~
#>  3 sales      listings    0.930  0.921   0.937  83.0   1083 0.       Perce~
#>  4 sales      inventory  -0.385 -0.434  -0.333 -13.7   1080 0.       Perce~
#>  5 volume     median      0.550  0.509   0.588  22.7   1195 0.       Perce~
#>  6 volume     listings    0.898  0.886   0.909  67.1   1083 0.       Perce~
#>  7 volume     inventory  -0.368 -0.419  -0.316 -13.0   1080 0.       Perce~
#>  8 median     listings    0.403  0.352   0.451  14.5   1083 0.       Perce~
#>  9 median     inventory  -0.203 -0.259  -0.145  -6.80  1080 1.70e-11 Perce~
#> 10 listings   inventory  -0.163 -0.220  -0.104  -5.42  1080 7.25e- 8 Perce~
#> # ... with 1 more variable: nobs <int>

Note that if cor.vars are not specified, all numeric variables will be used. Moreover, you can also use abbreviations to specify what output you want in return.

# for reproducibility
set.seed(123)

# show four digits in a tibble
options(pillar.sigfig = 4)

# getting the correlation coefficient matrix
ggstatsplot::ggcorrmat(
  data = iris, # all numeric variables from data will be used
  type = "np", # non-parametric
  output = "dataframe"
)
#> # A tibble: 6 x 9
#>   parameter1 parameter2     rho  ci_low   ci_high       s         p method  nobs
#>   <chr>      <chr>        <dbl>   <dbl>     <dbl>   <dbl>     <dbl> <chr>  <int>
#> 1 Sepal.Len~ Sepal.Wid~ -0.1668 -0.3185 -0.006695 656283. 4.137e- 2 Spear~   150
#> 2 Sepal.Len~ Petal.Len~  0.8819  0.8404  0.9131    66429. 3.443e-50 Spear~   150
#> 3 Sepal.Len~ Petal.Wid~  0.8343  0.7781  0.8773    93208. 4.189e-40 Spear~   150
#> 4 Sepal.Wid~ Petal.Len~ -0.3096 -0.4477 -0.1572   736637. 1.154e- 4 Spear~   150
#> 5 Sepal.Wid~ Petal.Wid~ -0.2890 -0.4294 -0.1350   725048. 3.343e- 4 Spear~   150
#> 6 Petal.Len~ Petal.Wid~  0.9377  0.9149  0.9545    35061. 8.157e-70 Spear~   150

Grouped analysis with `grouped_ggcorrmat`

What if we want to do the same analysis separately for each quality of the diamond cut (Fair, Good, Very Good, Premium, Ideal)?

ggstatsplot provides a special helper function for such instances: grouped_ggcorrmat. This is merely a wrapper function around ggstatsplot::combine_plots. It applies ggcorrmat across all levels of a specified grouping variable and then combines list of individual plots into a single plot. Note that the grouping variable can be anything: conditions in a given study, groups in a study sample, different studies, etc.

# for reproducibility
set.seed(123)

# let's use just 5% of the data to speed it up
ggstatsplot::grouped_ggcorrmat(
  # arguments relevant for ggstatsplot::ggcorrmat
  data = dplyr::sample_frac(tbl = ggplot2::diamonds, size = 0.05),
  type = "robust", # percentage bend correlation coefficient
  beta = 0.2, # bending constant
  p.adjust.method = "holm", # method to adjust p-values for multiple comparisons
  grouping.var = cut,
  title.prefix = "Quality of cut",
  cor.vars = c(carat, depth:z),
  cor.vars.names = c(
    "carat",
    "total depth",
    "table",
    "price",
    "length (in mm)",
    "width (in mm)",
    "depth (in mm)"
  ),
  lab.size = 3.5,
  # arguments relevant for ggstatsplot::combine_plots
  title.text = "Relationship between diamond attributes and price across cut",
  title.args = list(size = 16, color = "red"),
  caption.text = "Dataset: Diamonds from ggplot2 package",
  caption.args = list(size = 14, color = "blue"),
  plotgrid.args = list(
    labels = c("(a)", "(b)", "(c)", "(d)", "(e)"),
    nrow = 3,
    ncol = 2
  )
)

Note that this function also makes it easy to run the same correlation matrix across different levels of a factor/grouping variable.

# for reproducibility
set.seed(123)

# let's obtain correlation coefficients with their CIs
ggstatsplot::grouped_ggcorrmat(
  data = ggplot2::msleep,
  grouping.var = vore,
  output = "dataframe"
)
#> # A tibble: 60 x 11
#>    vore  parameter1 parameter2       r  ci_low  ci_high         t    df
#>    <chr> <chr>      <chr>        <dbl>   <dbl>    <dbl>     <dbl> <int>
#>  1 carni sleep_tot~ sleep_rem   0.9189  0.6864  0.9810   6.589e+0     8
#>  2 carni sleep_tot~ sleep_cyc~  0.3764 -0.7574  0.9449   7.038e-1     3
#>  3 carni sleep_tot~ awake      -1.000  -1.000  -1.000   -1.386e+3    17
#>  4 carni sleep_tot~ brainwt    -0.5244 -0.8815  0.2144  -1.629e+0     7
#>  5 carni sleep_tot~ bodywt     -0.4427 -0.7468  0.01441 -2.036e+0    17
#>  6 carni sleep_rem  sleep_cyc~  0.1216 -0.8521  0.9066   2.122e-1     3
#>  7 carni sleep_rem  awake      -0.9189 -0.9810 -0.6865  -6.589e+0     8
#>  8 carni sleep_rem  brainwt    -0.5006 -0.9331  0.5237  -1.157e+0     4
#>  9 carni sleep_rem  bodywt     -0.4786 -0.8516  0.2162  -1.542e+0     8
#> 10 carni sleep_cyc~ awake      -0.3764 -0.9449  0.7574  -7.038e-1     3
#> # ... with 50 more rows, and 3 more variables: p <dbl>, method <chr>,
#> #   nobs <int>

Grouped analysis with `ggcorrmat` + `purrr`

Although grouped_ function is good for quickly exploring the data, it reduces the flexibility with which this function can be used. This is the because the common parameters used are applied to plots corresponding to all levels of the grouping variable and there is no way to customize the arguments for different levels of the grouping variable. We will see how this can be done using the purrr package.

See the associated vignette here: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html

Summary of tests

Following tests are carried out for each type of analyses-

Type	Test	CI?
Parametric	Pearson’s correlation coefficient	Yes
Non-parametric	Spearman’s rank correlation coefficient	Yes
Robust	Percentage bend correlation coefficient	Yes
Bayes Factor	Pearson’s correlation coefficient	Yes

Suggestions

If you find any bugs or have any suggestions/remarks, please file an issue on GitHub: https://github.com/IndrajeetPatil/ggstatsplot/issues

Session Information

For details, see- https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/session_info.html

ggcorrmat

Indrajeet Patil

2020-07-14

Correlation matrix plot with `ggcorrmat`

Dataframe containing statistics with `ggcorrmat`

Grouped analysis with `grouped_ggcorrmat`

Grouped analysis with `ggcorrmat` + `purrr`

Summary of tests

Suggestions

Session Information

ggcorrmat

Indrajeet Patil

2020-07-14

Correlation matrix plot with ggcorrmat

Dataframe containing statistics with ggcorrmat

Grouped analysis with grouped_ggcorrmat

Grouped analysis with ggcorrmat + purrr

Summary of tests

Suggestions

Session Information

Correlation matrix plot with `ggcorrmat`

Dataframe containing statistics with `ggcorrmat`

Grouped analysis with `grouped_ggcorrmat`

Grouped analysis with `ggcorrmat` + `purrr`