ggcorrmat: Visualization of a correlation matrix

View source: R/ggcorrmat.R

ggcorrmatR Documentation

Visualization of a correlation matrix

Description

Correlation matrix or a dataframe containing results from pairwise correlation tests. The package internally uses ggcorrplot::ggcorrplot for creating the visualization matrix, while the correlation analysis is carried out using the correlation::correlation function.

Usage

ggcorrmat(
  data,
  cor.vars = NULL,
  cor.vars.names = NULL,
  output = "plot",
  matrix.type = "upper",
  type = "parametric",
  tr = 0.2,
  partial = FALSE,
  k = 2L,
  sig.level = 0.05,
  conf.level = 0.95,
  bf.prior = 0.707,
  p.adjust.method = "holm",
  pch = "cross",
  ggcorrplot.args = list(method = "square", outline.color = "black", pch.cex = 14),
  package = "RColorBrewer",
  palette = "Dark2",
  colors = c("#E69F00", "white", "#009E73"),
  ggtheme = ggstatsplot::theme_ggstatsplot(),
  ggplot.component = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ...
)

Arguments

data

Dataframe from which variables specified are preferentially to be taken.

cor.vars

List of variables for which the correlation matrix is to be computed and visualized. If NULL (default), all numeric variables from data will be used.

cor.vars.names

Optional list of names to be used for cor.vars. The names should be entered in the same order.

output

Character that decides expected output from this function. If "plot", the visualization matrix will be returned. If "dataframe" (or literally anything other than "plot"), a dataframe containing all details from statistical analyses (e.g., correlation coefficients, statistic values, p-values, no. of observations, etc.) will be returned.

matrix.type

Character, "upper" (default), "lower", or "full", display full matrix, lower triangular or upper triangular matrix.

type

A character specifying the type of statistical approach:

  • "parametric"

  • "nonparametric"

  • "robust"

  • "bayes"

You can specify just the initial letter.

tr

Trim level for the mean when carrying out robust tests. In case of an error, try reducing the value of tr, which is by default set to 0.2. Lowering the value might help.

partial

Can be TRUE for partial correlations. For Bayesian partial correlations, "full" instead of pseudo-Bayesian partial correlations (i.e., Bayesian correlation based on frequentist partialization) are returned.

k

Number of digits after decimal point (should be an integer) (Default: k = 2L).

sig.level

Significance level (Default: 0.05). If the p-value in p-value matrix is bigger than sig.level, then the corresponding correlation coefficient is regarded as insignificant and flagged as such in the plot. Relevant only when output = "plot".

conf.level

Scalar between 0 and 1. If unspecified, the defaults return 95% confidence/credible intervals (0.95).

bf.prior

A number between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: "medium", "wide", and "ultrawide", corresponding to r scale values of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value corresponds to scale for fixed effects.

p.adjust.method

Adjustment method for p-values for multiple comparisons. Possible methods are: "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

pch

Decides the point shape to be used for insignificant correlation coefficients (only valid when insig = "pch"). Default: pch = "cross".

ggcorrplot.args

A list of additional (mostly aesthetic) arguments that will be passed to ggcorrplot::ggcorrplot function. The list should avoid any of the following arguments since they are already internally being used: corr, method, p.mat, sig.level, ggtheme, colors, lab, pch, legend.title, digits.

package, palette

Name of the package from which the given palette is to be extracted. The available palettes and packages can be checked by running View(paletteer::palettes_d_names).

colors

A vector of 3 colors for low, mid, and high correlation values. If set to NULL, manual specification of colors will be turned off and 3 colors from the specified palette from package will be selected.

ggtheme

A {ggplot2} theme. Default value is ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well.

ggplot.component

A ggplot component to be added to the plot prepared by {ggstatsplot}. This argument is primarily helpful for grouped_ variants of all primary functions. Default is NULL. The argument should be entered as a {ggplot2} function or a list of {ggplot2} functions.

title

The text for the plot title.

subtitle

The text for the plot subtitle. Will work only if results.subtitle = FALSE.

caption

The text for the plot caption. This argument is relevant only if bf.message = FALSE.

...

Currently ignored.

Details

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

See Also

grouped_ggcorrmat ggscatterstats grouped_ggscatterstats

Examples

# for reproducibility
set.seed(123)
library(ggstatsplot)

# to get a plot (assumes that `ggcorrplot` is installed)
if (require("ggcorrplot")) ggcorrmat(iris)

# to get a dataframe
ggcorrmat(
  data = ggplot2::msleep,
  cor.vars = sleep_total:bodywt,
  partial = TRUE,
  output = "dataframe"
)

ggstatsplot documentation built on May 21, 2022, 5:05 p.m.