network_plot: Network plot of a correlation matrix

In metan: Multi Environment Trials Analysis

Network plot of a correlation matrix

Description

Produces a network plot of a correlation matrix or an object computed with corr_coef(). Variables that are more highly correlated appear closer together and are joined by stronger (more opaque) and wider paths. The proximity of the points is determined using multidimensional clustering, also known as principal coordinates analysis (Gower, 1966). The color of the paths also indicates the sign of the correlation (blue for positive and red for negative).

Usage

network_plot(
  model,
  min_cor = NULL,
  show = c("signif", "all"),
  p_val = 0.05,
  legend = c("full", "range"),
  colours = c("red", "white", "blue"),
  legend_width = 1,
  legend_height = 15,
  legend_position = c("right", "left", "top", "bottom"),
  curved = TRUE,
  angle = 90,
  curvature = 0.5,
  expand_x = 0.25,
  expand_y = 0.25
)

Arguments

model	A model computed with corr_coef() or a symmetric matrix, often produced with stats::cor().
min_cor	Number to indicate the minimum value of correlations to plot (0-1 in absolute terms). By default, all the correlations are plotted when model is a matrix, and significant correlations (p-value < 0.05) when model is an object computed with corr_coef().
show	The correlations to be shown when model is an object computed with corr_coef(). Either "signif" (default) to show only significant correlations or "all" to show all the correlations.
p_val	The p-value to indicate significant correlations. Defaults to 0.05.
legend	The type of legend. Either "full" (ranges from -1 to +1) or "range" (ranges according to the data range). Defaults to "full".
colours	A vector of colors to use for n-color gradient.
legend_width	The width of the legend (considering position = "right")
legend_height	The height of the legend (considering position = "right")
legend_position	The legend position. Defaults to "right".
curved	Shows curved paths? Defaults to TRUE.
angle	A numeric value between 0 and 180, giving an amount to skew the control points of the curve. Values less than 90 skew the curve towards the start point and values greater than 90 skew the curve towards the end point.
curvature	A numeric value giving the amount of curvature. Negative values produce left-hand curves, positive values produce right-hand curves, and zero produces a straight line.
expand_x, expand_y	Vector of multiplicative range expansion factors. If length 1, both the lower and upper limits of the scale are expanded outwards by mult. If length 2, the lower limit is expanded by mult[1] and the upper limit by mult[2].

Value

A ggplot object

References

Gower, J.C. 1966. Some Distance Properties of Latent Root and Vector Methods Used in Multivariate Analysis. Biometrika 53(3/4): 325–338. doi: 10.2307/2333639

Examples

cor <- corr_coef(iris)
network_plot(cor)
network_plot(cor,
             show = "all",
             curved = FALSE,
             legend_position = "bottom",
             legend = "range")

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