ggstatsplot (version 0.1.4)

grouped_ggcorrmat: Visualization of a correlalogram (or correlation matrix) for all levels of a grouping variable

Description

Helper function for ggstatsplot::ggcorrmat to apply this function across multiple levels of a given factor and combining the resulting plots using ggstatsplot::combine_plots.

Usage

grouped_ggcorrmat(
  data,
  cor.vars = NULL,
  cor.vars.names = NULL,
  grouping.var,
  title.prefix = NULL,
  output = "plot",
  matrix.type = "full",
  method = "square",
  corr.method = "pearson",
  type = NULL,
  exact = FALSE,
  continuity = TRUE,
  beta = 0.1,
  digits = 2,
  k = NULL,
  sig.level = 0.05,
  conf.level = 0.95,
  p.adjust.method = "none",
  hc.order = FALSE,
  hc.method = "complete",
  lab = TRUE,
  package = "RColorBrewer",
  palette = "Dark2",
  direction = 1,
  colors = c("#E69F00", "white", "#009E73"),
  outline.color = "black",
  ggtheme = ggplot2::theme_bw(),
  ggstatsplot.layer = TRUE,
  subtitle = NULL,
  caption = NULL,
  caption.default = TRUE,
  lab.col = "black",
  lab.size = 5,
  insig = "pch",
  pch = 4,
  pch.col = "black",
  pch.cex = 11,
  tl.cex = 12,
  tl.col = "black",
  tl.srt = 45,
  messages = TRUE,
  return = 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.

grouping.var

A single grouping variable (can be entered either as a bare name x or as a string "x").

title.prefix

Character string specifying the prefix text for the fixed plot title (name of each factor level) (Default: NULL). If NULL, the variable name entered for grouping.var will be used.

output

Character that decides expected output from this function: "plot" (for visualization matrix) or "correlations" (or "corr" or "r"; for correlation matrix) or "p-values" (or "p.values" or "p"; for a matrix of p-values) or "ci" (for a tibble with confidence intervals for unique correlation pairs; not available for robust correlation) or "n" (or "sample.size" for a tibble with sample sizes for each correlation pair).

matrix.type

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

method

Character argument that decides the visualization method of correlation matrix to be used. Allowed values are "square" (default), "circle"

corr.method

A character string indicating which correlation coefficient is to be computed ("pearson" (default) or "kendall" or "spearman"). "robust" can also be entered but only if output argument is set to either "correlations" or "p-values". The robust correlation used is percentage bend correlation (see ?WRS2::pball). Abbreviations will also work: "p" (for parametric/Pearson's r), "np" (nonparametric/Spearman's rho), "r" (robust).

type

A character string indicating which correlation coefficient is to be computed ("pearson" (default) or "kendall" or "spearman"). "robust" can also be entered but only if output argument is set to either "correlations" or "p-values". The robust correlation used is percentage bend correlation (see ?WRS2::pball). Abbreviations will also work: "p" (for parametric/Pearson's r), "np" (nonparametric/Spearman's rho), "r" (robust).

exact

A logical indicating whether an exact p-value should be computed. Used for Spearman's rho. For more details, see ?stats::cor.test.

continuity

A logical. If TRUE, a continuity correction is used for Spearman's rho when not computed exactly (Default: TRUE).

beta

A numeric bending constant for percentage bend robust correlation coefficient (Default: 0.1).

digits

Decides the number of decimal digits to be displayed (Default: 2).

k

Decides the number of decimal digits to be displayed (Default: 2).

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. This argument is relevant only when output = "plot".

conf.level

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

p.adjust.method

What adjustment for multiple tests should be used? ("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"). See stats::p.adjust for details about why to use "holm" rather than "bonferroni"). Default is "none". If adjusted p-values are displayed in the visualization of correlation matrix, the adjusted p-values will be used for the upper triangle, while unadjusted p-values will be used for the lower triangle of the matrix.

hc.order

Logical value. If TRUE, correlation matrix will be hc.ordered using hclust function (Default is FALSE).

hc.method

The agglomeration method to be used in hclust (see ?hclust).

lab

Logical value. If TRUE, correlation coefficient values will be displayed in the plot.

package

Name of package from which the palette is desired as string or symbol.

palette

Name of palette as string or symbol.

direction

Either 1 or -1. If -1 the palette will be reversed.

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.

outline.color

The outline color of square or circle. Default value is "gray".

ggtheme

A function, ggplot2 theme name. Default value is ggplot2::theme_bw(). Any of the ggplot2 themes, or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.).

ggstatsplot.layer

Logical that decides whether theme_ggstatsplot theme elements are to be displayed along with the selected ggtheme (Default: TRUE). theme_ggstatsplot is an opinionated theme layer that override some aspects of the selected ggtheme.

subtitle

The text for the plot subtitle.

caption

The text for the plot caption. If NULL, a default caption will be shown.

caption.default

Logical that decides whether the default caption should be shown (default: TRUE).

lab.col

Color to be used for the correlation coefficient labels (applicable only when lab = TRUE).

lab.size

Size to be used for the correlation coefficient labels (applicable only when lab = TRUE).

insig

Character used to show specialized insignificant correlation coefficients ("pch" (default) or "blank"). If "blank", the corresponding glyphs will be removed; if "pch" is used, characters (see ?pch for details) will be added on the corresponding glyphs.

pch

Decides the glyphs (read point shapes) to be used for insignificant correlation coefficients (only valid when insig = "pch"). Default value is pch = 4.

pch.col

The color and the cex (size) of pch (only valid when insig = "pch"). Defaults are pch.col = "#F0E442" and pch.cex = 10.

pch.cex

The color and the cex (size) of pch (only valid when insig = "pch"). Defaults are pch.col = "#F0E442" and pch.cex = 10.

tl.cex

The size, the color, and the string rotation of text label (variable names, i.e.).

tl.col

The size, the color, and the string rotation of text label (variable names, i.e.).

tl.srt

The size, the color, and the string rotation of text label (variable names, i.e.).

messages

Decides whether messages references, notes, and warnings are to be displayed (Default: TRUE).

return

Character that decides expected output from this function: "plot" (for visualization matrix) or "correlations" (or "corr" or "r"; for correlation matrix) or "p-values" (or "p.values" or "p"; for a matrix of p-values) or "ci" (for a tibble with confidence intervals for unique correlation pairs; not available for robust correlation) or "n" (or "sample.size" for a tibble with sample sizes for each correlation pair).

...

Arguments passed on to combine_plots

title.text

String or plotmath expression to be drawn as title for the combined plot.

title.color

Text color for title.

title.size

Point size of title text.

title.vjust

Vertical justification for title. Default = 0.5 (centered on y). 0 = baseline at y, 1 = ascender at y.

title.hjust

Horizontal justification for title. Default = 0.5 (centered on x). 0 = flush-left at x, 1 = flush-right.

title.fontface

The font face ("plain", "bold" (default), "italic", "bold.italic") for title.

caption.text

String or plotmath expression to be drawn as the caption for the combined plot.

caption.color

Text color for caption.

caption.size

Point size of title text.

caption.vjust

Vertical justification for caption. Default = 0.5 (centered on y). 0 = baseline at y, 1 = ascender at y.

caption.hjust

Horizontal justification for caption. Default = 0.5 (centered on x). 0 = flush-left at x, 1 = flush-right.

caption.fontface

The font face ("plain" (default), "bold", "italic", "bold.italic") for caption.

sub.text

The label with which the combined plot should be annotated. Can be a plotmath expression.

sub.color

Text color for annotation label (Default: "black").

sub.size

Point size of annotation text (Default: 12).

sub.x

The x position of annotation label (Default: 0.5).

sub.y

The y position of annotation label (Default: 0.5).

sub.hjust

Horizontal justification for annotation label (Default: 0.5).

sub.vjust

Vertical justification for annotation label (Default: 0.5).

sub.vpadding

Vertical padding. The total vertical space added to the label, given in grid units. By default, this is added equally above and below the label. However, by changing the y and vjust parameters, this can be changed (Default: ggplot2::unit(1, "lines")).

sub.fontface

The font face ("plain" (default), "bold", "italic", "bold.italic") for the annotation label.

sub.angle

Angle at which annotation label is to be drawn (Default: 0).

sub.lineheight

Line height of annotation label.

title.caption.rel.heights

Numerical vector of relative columns heights while combining (title, plot, caption).

title.rel.heights

Numerical vector of relative columns heights while combining (title, plot).

caption.rel.heights

Numerical vector of relative columns heights while combining (plot, caption).

Value

Correlation matrix plot or correlation coefficient matrix or matrix of p-values.

References

https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcorrmat.html

See Also

ggcorrmat, ggscatterstats, grouped_ggscatterstats

Examples

# NOT RUN {
# for reproducibility
set.seed(123)

# for plot
# (without specifying needed variables; all numeric variables will be used)
ggstatsplot::grouped_ggcorrmat(
  data = ggplot2::msleep,
  grouping.var = vore
)

# for getting plot
ggstatsplot::grouped_ggcorrmat(
  data = ggplot2::msleep,
  grouping.var = vore,
  cor.vars = sleep_total:bodywt,
  corr.method = "r",
  p.adjust.method = "holm",
  colors = NULL,
  package = "wesanderson",
  palette = "BottleRocket2",
  nrow = 2
)

# for getting correlations
ggstatsplot::grouped_ggcorrmat(
  data = ggplot2::msleep,
  grouping.var = vore,
  cor.vars = sleep_total:bodywt,
  output = "correlations"
)

# for getting confidence intervals
# confidence intervals are not available for **robust** correlation
ggstatsplot::grouped_ggcorrmat(
  data = datasets::iris,
  grouping.var = Species,
  corr.method = "r",
  p.adjust.method = "holm",
  cor.vars = Sepal.Length:Petal.Width,
  output = "ci"
)
# }