Skip to contents

Correlation and partial correlation networks.

Source: R/DPI.R
cor_net.Rd

Correlation and partial correlation networks (also called Gaussian graphical models, GGMs).

Usage

cor_net(
  data,
  index = c("cor", "pcor"),
  show.label = TRUE,
  show.insig = FALSE,
  show.cutoff = FALSE,
  faded = FALSE,
  node.text.size = 1.2,
  node.group = NULL,
  node.color = NULL,
  edge.color.pos = "#0571B0",
  edge.color.neg = "#CA0020",
  edge.color.non = "#EEEEEEEE",
  edge.width.min = "sig",
  edge.width.max = NULL,
  edge.label.mrg = 0.01,
  file = NULL,
  width = 6,
  height = 4,
  dpi = 500,
  ...
)

Arguments

data

Data.

index

Type of graph: "cor" (raw correlation network) or "pcor" (partial correlation network). Defaults to "cor".

show.label

Show labels of correlation coefficients and their significance on edges. Defaults to TRUE.

show.insig

Show edges with insignificant correlations (p > 0.05). Defaults to FALSE. To change significance level, please set alpha (defaults to alpha=0.05).

show.cutoff

Show cut-off values of correlations. Defaults to FALSE.

faded

Transparency of edges according to the effect size of correlation. Defaults to FALSE.

node.text.size

Scalar on the font size of node (variable) labels. Defaults to 1.2.

node.group

A list that indicates which nodes belong together, with each element of list as a vector of integers identifying the column numbers of variables that belong together.

node.color

A vector with a color for each element in node.group, or a color for each node.

edge.color.pos

Color for (significant) positive values. Defaults to "#0571B0" (blue in ColorBrewer's RdBu palette).

edge.color.neg

Color for (significant) negative values. Defaults to "#CA0020" (red in ColorBrewer's RdBu palette).

edge.color.non

Color for insignificant values. Defaults to "#EEEEEEEE" (faded light grey).

edge.width.min

Minimum value of edge strength to scale all edge widths. Defaults to sig (the threshold of significant values).

edge.width.max

Maximum value of edge strength to scale all edge widths. Defaults to NULL (for undirected correlation networks) and 1.5 (for directed acyclic networks to better display arrows).

edge.label.mrg

Margin of the background box around the edge label. Defaults to 0.01.

file

File name of saved plot (".png" or ".pdf").

width, height

Width and height (in inches) of saved plot. Defaults to 6 and 4.

dpi

Dots per inch (figure resolution). Defaults to 500.

...

Arguments passed on to qgraph().

Value

Return a list (class cor.net) of (partial) correlation results and qgraph object.

See also

S3method.network

DPI_dag()

BNs_dag()

Examples

# correlation network
cor_net(airquality)
#> Displaying Correlation Network

cor_net(airquality, show.insig=TRUE)
#> Displaying Correlation Network


# partial correlation network
cor_net(airquality, "pcor")
#> Displaying Partial Correlation Network

cor_net(airquality, "pcor", show.insig=TRUE)
#> Displaying Partial Correlation Network


# modify ggplot attributes
p = cor_net(airquality, "pcor")
gg = plot(p)  # return a ggplot object
gg + labs(title="Partial Correlation Network")