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
.
grouped_ggcorrmat(data, cor.vars = NULL, cor.vars.names = NULL,
grouping.var, title.prefix = "Group", 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, 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, axis.text.x.margin.t = 0, axis.text.x.margin.r = 0,
axis.text.x.margin.b = 0, axis.text.x.margin.l = 0,
messages = TRUE, ...)
Dataframe from which variables specified are preferentially to be taken.
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.
Optional list of names to be used for cor.vars
. The
names should be entered in the same order.
Grouping variable.
Character specifying the prefix text for the fixed plot
title (name of each factor level) (Default: "Group"
).
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).
Character, "full"
(default), "upper"
or "lower"
,
display full matrix, lower triangular or upper triangular matrix.
Character argument that decides the visualization method of
correlation matrix to be used. Allowed values are "square"
(default),
"circle"
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).
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).
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
.
A logical. If TRUE
, a continuity correction is used for
Kendall's tau and Spearman's rho when not computed exactly (Default:
TRUE
).
A numeric bending constant for robust correlation coefficient
(Default: 0.1
).
Decides the number of decimal digits to be displayed
(Default: 2
).
Decides the number of decimal digits to be displayed
(Default: 2
).
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"
.
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.
Logical value. If TRUE
, correlation matrix will be
hc.ordered using hclust
function (Default is FALSE
).
The agglomeration method to be used in hclust
(see
?hclust
).
Logical value. If TRUE
, correlation coefficient values will be
displayed in the plot.
Name of package from which the palette is desired as string or symbol.
Name of palette as string or symbol.
Either 1
or -1
. If -1
the palette will be reversed.
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.
The outline color of square or circle. Default value is
"gray"
.
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_economist()
,
hrbrthemes::theme_ipsum_ps()
, ggthemes::theme_fivethirtyeight()
, etc.).
Logical that decides whether theme_ggstatsplot
theme elements are to be displayed along with the selected ggtheme
(Default: TRUE
).
The text for the plot subtitle.
The text for the plot caption. If not specified (if it is
NULL
, i.e.), a default caption will be shown.
Logical decides whether the default caption should be shown.
Color to be used for the correlation coefficient labels
(applicable only when lab = TRUE
).
Size to be used for the correlation coefficient labels
(applicable only when lab = TRUE
).
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.
Decides the glyphs (read point shapes) to be used for
insignificant correlation coefficients (only valid when insig = "pch"
).
Default value is pch = 4
.
The color and the cex (size) of pch
(only valid when
insig = "pch"
). Defaults are pch.col = "#F0E442"
and pch.cex = 10
.
The color and the cex (size) of pch
(only valid when
insig = "pch"
). Defaults are pch.col = "#F0E442"
and pch.cex = 10
.
The size, the color, and the string rotation of text label (variable names, i.e.).
The size, the color, and the string rotation of text label (variable names, i.e.).
The size, the color, and the string rotation of text label (variable names, i.e.).
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.).
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.).
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.).
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.).
Decides whether messages references, notes, and warnings are
to be displayed (Default: TRUE
).
Arguments passed on to combine_plots
String or plotmath expression to be drawn as title for the combined plot.
Text color for title.
Point size of title text.
Vertical justification for title. Default = 0.5
(centered on y
). 0
= baseline at y
, 1
= ascender at y
.
Horizontal justification for title. Default = 0.5
(centered on x
). 0
= flush-left at x, 1
= flush-right.
The font face ("plain"
, "bold"
(default),
"italic"
, "bold.italic"
) for title.
String or plotmath expression to be drawn as the caption for the combined plot.
Text color for caption.
Point size of title text.
Vertical justification for caption. Default = 0.5
(centered on y). 0
= baseline at y, 1
= ascender at y.
Horizontal justification for caption. Default = 0.5
(centered on x). 0
= flush-left at x, 1
= flush-right.
The font face ("plain"
(default), "bold"
,
"italic"
, "bold.italic"
) for caption.
The label with which the combined plot should be annotated. Can be a plotmath expression.
Text color for annotation label (Default: "black"
).
Point size of annotation text (Default: 12
).
The x position of annotation label (Default: 0.5
).
The y position of annotation label (Default: 0.5
).
Horizontal justification for annotation label (Default:
0.5
).
Vertical justification for annotation label (Default:
0.5
).
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")
).
The font face ("plain"
(default), "bold"
, "italic"
,
"bold.italic"
) for the annotation label.
Angle at which annotation label is to be drawn (Default:
0
).
Line height of annotation label.
Numerical vector of relative columns heights while combining (title, plot, caption).
Numerical vector of relative columns heights while combining (title, plot).
Numerical vector of relative columns heights while combining (plot, caption).
Correlation matrix plot or correlation coefficient matrix or matrix of p-values.
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcorrmat.html
# NOT RUN {
# for reproducibility
set.seed(123)
# for plot
# (without specifiying 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"
)
# }
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