ggstatsplot (version 0.0.5)

grouped_ggcorrmat: Visualization of a correlalogram (or correlation matrix) using 'ggplot2'/'ggcorrplot' 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, cor.vars.names = NULL, grouping.var,
  title.prefix = "Group", output = "plot", type = "full",
  method = "square", corr.method = "pearson", exact = FALSE,
  continuity = TRUE, beta = 0.1, digits = 2, sig.level = 0.05,
  hc.order = FALSE, hc.method = "complete", lab = TRUE,
  colors = c("#E69F00", "white", "#009E73"), outline.color = "black",
  ggtheme = ggplot2::theme_bw, ggstatsplot.theme = 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, axis.text.x.margin.t = 0, axis.text.x.margin.r = 0,
  axis.text.x.margin.b = 0, axis.text.x.margin.l = 0,
  legend.title.margin = FALSE, t.margin = unit(0, "mm"),
  b.margin = unit(3, "mm"), messages = TRUE, ...)

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.

cor.vars.names

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

grouping.var

Grouping variable.

title.prefix

Character specifying the prefix text for the fixed plot title (name of each factor level) (Default: "Group").

output

Expected output from this function: "plot" (visualization matrix) or "correlations" (correlation matrix) or "p-values" (matrix of p-values).

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 not work.

exact

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

continuity

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

beta

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

digits

Decides the number of decimal digits to be added into the plot (Default: 2).

sig.level

Significance level (Default: 0.05). If the p-value in p-mat (p-value matrix) is bigger than sig.level, then the corresponding correlation coefficient is regarded as insignificant.

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.

colors

A vector of 3 colors for low, mid, and high correlation values.

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. Allowed values are the official ggplot2 themes, including theme_grey, theme_minimal, theme_classic, theme_void, etc.

ggstatsplot.theme

A logical. Decides whether default theme for ggstatsplot, which is theme_mprl, is to be overlaid on the entered theme (Default: ggstatsplot.theme = TRUE).

subtitle

The text for the plot subtitle.

caption

The text for the plot caption. If not specified (if it is NULL, i.e.), a default caption will be shown.

caption.default

Logical decides whether the default caption should be shown.

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.).

axis.text.x.margin.t

Margins between x-axis and the variable name texts (t: top, r: right, b: bottom, l:left), especially useful in case the names are slanted, i.e. when the tl.srt is between 45 and 75 (Defaults: 0, 0, 0, 0, resp.).

axis.text.x.margin.r

Margins between x-axis and the variable name texts (t: top, r: right, b: bottom, l:left), especially useful in case the names are slanted, i.e. when the tl.srt is between 45 and 75 (Defaults: 0, 0, 0, 0, resp.).

axis.text.x.margin.b

Margins between x-axis and the variable name texts (t: top, r: right, b: bottom, l:left), especially useful in case the names are slanted, i.e. when the tl.srt is between 45 and 75 (Defaults: 0, 0, 0, 0, resp.).

axis.text.x.margin.l

Margins between x-axis and the variable name texts (t: top, r: right, b: bottom, l:left), especially useful in case the names are slanted, i.e. when the tl.srt is between 45 and 75 (Defaults: 0, 0, 0, 0, resp.).

legend.title.margin

Logical indicating whether to adjust the margin between legend title and the colorbar (Default: FALSE).

t.margin

Margins in grid units. For more details, see ?grid::unit().

b.margin

Margins in grid units. For more details, see ?grid::unit().

messages

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

...

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: grid::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).

References

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

See Also

ggcorrmat ggscatterstats grouped_ggscatterstats

Examples

Run this code
# NOT RUN {
# for getting correlations
ggstatsplot::grouped_ggcorrmat(
  data = datasets::iris,
  grouping.var = Species,
  cor.vars = Sepal.Length:Petal.Width,
  output = "plot",
  nrow = 3,
  ncol = 1
)

# for getting correlations
ggstatsplot::grouped_ggcorrmat(
  data = datasets::iris,
  grouping.var = Species,
  cor.vars = Sepal.Length:Petal.Width,
  output = "correlations"
)
# }

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