corr_plot: Visualization of a correlation matrix

In metan: Multi Environment Trials Analysis

Visualization of a correlation matrix

Description

Graphical and numerical visualization of a correlation matrix

Usage

corr_plot(
  .data,
  ...,
  col.by = NULL,
  upper = "corr",
  lower = "scatter",
  decimal.mark = ".",
  axis.labels = FALSE,
  show.labels.in = "show",
  size.axis.label = 12,
  size.varnames = 12,
  col.varnames = "black",
  diag = TRUE,
  diag.type = "histogram",
  bins = 20,
  col.diag = "gray",
  alpha.diag = 1,
  col.up.panel = "gray",
  col.lw.panel = "gray",
  col.dia.panel = "gray",
  prob = 0.05,
  col.sign = "green",
  alpha.sign = 0.15,
  lab.position = "tr",
  progress = NULL,
  smooth = FALSE,
  col.smooth = "red",
  confint = TRUE,
  size.point = 1,
  shape.point = 19,
  alpha.point = 0.7,
  fill.point = NULL,
  col.point = "black",
  size.line = 0.5,
  minsize = 2,
  maxsize = 3,
  pan.spacing = 0.15,
  digits = 2,
  export = FALSE,
  file.type = "pdf",
  file.name = NULL,
  width = 8,
  height = 7,
  resolution = 300
)

Arguments

.data	The data. Should, preferentially, contain numeric variables only. If .data has factor-columns, these columns will be deleted with a warning message.
...	Variables to use in the correlation. If no variable is informed all the numeric variables from .data are used.
col.by	A categorical variable to map the color of the points by. Defaults to NULL.
upper	The visualization method for the upper triangular correlation matrix. Must be one of 'corr' (numeric values), 'scatter' (the scatterplot for each pairwise combination), or NULL to set a blank diagonal.
lower	The visualization method for the lower triangular correlation matrix. Must be one of 'corr' (numeric values), 'scatter' (the scatterplot for each pairwise combination), or NULL to set a blank diagonal.
decimal.mark	The decimal mark. Defaults to ".".
axis.labels	Should the axis labels be shown in the plot? Set to FALSE.
show.labels.in	Where to show the axis labels. Defaults to "show" bottom and left. Use "diag" to show the labels on the diagonal. In this case, the diagonal layer (boxplot, density or histogram) will be overwritten.
size.axis.label	The size of the text for axis labels if axis.labels = TRUE. Defaults to 12.
size.varnames	The size of the text for variable names. Defaults to 12.
col.varnames	The color of the text for variable names. Defaults to "black".
diag	Should the diagonal be shown?
diag.type	The type of plot to show in the diagonal if diag TRUE. It must be one of the 'histogram' (to show an histogram), 'density' to show the Kernel density, or 'boxplot' (to show a boxplot).
bins	The number of bins, Defaults to 20.
col.diag	If diag = TRUE then diagcol is the color for the distribution. Set to gray.
alpha.diag	Alpha-transparency scale (0-1) to make the diagonal plot transparent. 0 = fully transparent; 1 = full color. Set to 0.15
col.up.panel, col.lw.panel, col.dia.panel	The color for the upper, lower, and diagonal panels, respectively. Set to 'gray'.
prob	The probability of error. Significant correlations will be highlighted with '', '', and '' (0.05, 0.01, and 0.001, respectively). Scatterplots with significant correlations may be color-highlighted.
col.sign	The color that will highlight the significant correlations. Set to 'green'.
alpha.sign	Alpha-transparency scale (0-1) to make the plot area transparent. 0 = fully transparent; 1 = full color. Set to 0.15
lab.position	The position that the labels will appear. Set to 'tr', i.e., the legends will appear in the top and right of the plot. Other allowed options are 'tl' (top and left), 'br' (bottom and right), 'bl' (bottom and left).
progress	NULL (default) for a progress bar in interactive sessions with more than 15 plots, TRUE for a progress bar, FALSE for no progress bar.
smooth	Should a linear smooth line be shown in the scatterplots? Set to FALSE.
col.smooth	The color for the smooth line.
confint	Should a confidence band be shown with the smooth line? Set to TRUE.
size.point	The size of the points in the plot. Set to 0.5.
shape.point	The shape of the point, set to 1.
alpha.point	Alpha-transparency scale (0-1) to make the points transparent. 0 = fully transparent; 1 = full color. Set to 0.7
fill.point	The color to fill the points. Valid argument if points are between 21 and 25.
col.point	The color for the edge of the point, set to black.
size.line	The size of the line (smooth and diagonal).
minsize	The size of the letter that will represent the smallest correlation coefficient.
maxsize	The size of the letter that will represent the largest correlation coefficient.
pan.spacing	The space between the panels. Set to 0.15.
digits	The number of digits to show in the plot.
export	Logical argument. If TRUE, then the plot is exported to the current directory.
file.type	The format of the file if export = TRUE. Set to 'pdf'. Other possible values are *.tiff using file.type = 'tiff'.
file.name	The name of the plot when exported. Set to NULL, i.e., automatically.
width	The width of the plot, set to 8.
height	The height of the plot, set to 7.
resolution	The resolution of the plot if file.type = 'tiff' is used. Set to 300 (300 dpi).

Value

An object of class gg, ggmatrix.

Author(s)

Tiago Olivoto [e-mail]

Examples

library(metan)
dataset <- data_ge2 %>% select_cols(1:7)

# Default plot setting
corr_plot(dataset)

# Chosing variables to be correlated
corr_plot(dataset, PH, EH, EL)


# Axis labels, similar to the function pairs()
# Gray scale
corr_plot(dataset, PH, EH, EL,
          shape.point = 19,
          size.point = 2,
          alpha.point = 0.5,
          alpha.diag = 0,
          pan.spacing = 0,
          col.sign = 'gray',
          alpha.sign = 0.3,
          axis.labels = TRUE)

corr_plot(dataset, PH, EH, EL,
          prob = 0.01,
          shape.point = 21,
          col.point = 'black',
          fill.point = 'orange',
          size.point = 2,
          alpha.point = 0.6,
          maxsize = 4,
          minsize = 2,
          smooth = TRUE,
          size.line = 1,
          col.smooth = 'black',
          col.sign = 'cyan',
          col.up.panel = 'black',
          col.lw.panel = 'black',
          col.dia.panel = 'black',
          pan.spacing = 0,
          lab.position = 'tl')

metan documentation built on March 7, 2023, 5:34 p.m.