vizNetConnectogram — vizNetConnectogram • FCtools

Generate a Network Connectogram from a Vector of FC network or edge data

Usage

vizNetConnectogram(
  FC_dat,
  show.sig = T,
  title = NULL,
  title.size = 10,
  hot = "#F8766D",
  cold = "#00BFC4",
  node.text.size = 2,
  node.size = 2,
  node.color = "black",
  edge.thickness = 1.5,
  sig.color = "darkgrey",
  legend = T,
  legend.title = "Standardized Coefficient",
  legend.title.size = 6,
  legend.text.size = 5,
  expand = 1.1,
  limits,
  filename,
  width = 1000,
  height = 700
)

Arguments

show.sig: Logical. If TRUE, significant edges will be outlined with sig.color. Default is FALSE.
title: Character string for the plot title. Default is NULL (no title).
title.size: Numeric. Font size of the plot title. Default is 10.
hot: Character. Color used for positive edges and node highlights. Default is "#F8766D" (red).
cold: Character. Color used for negative edges and node highlights. Default is "#00BFC4" (teal).
node.text.size: Numeric. Size of the node label text. Default is 2.
node.size: Numeric. Size of the node points. Default is 2.
node.color: Character. Fill color of the node points. Default is "black".
edge.thickness: Numeric. Width of the edges (and node border stroke). Default is 2.
legend: Logical. If TRUE, a continuous color bar legend is added to the plot. Default is TRUE.
legend.title: Character string for the legend title. Default is "Standardized Coefficient".
legend.title.size: Numeric. Font size of the legend title. Default is 8.
legend.text.size: Numeric. Font size of the legend tick labels. Default is 5.
expand: Numeric. Multiplicative expansion factor applied to the x and y axis limits to prevent node labels from being clipped. Default is 1.1.
limits: Numeric vector of length 2. Color scale limits for the edge alpha and node alpha mappings. If not supplied, limits are set automatically to c(0, max(abs(weight))) inside the function.
filename: Character. Path/filename for the output PNG. If the argument is omitted entirely, no file is written.
width: Integer. Width of the saved PNG in pixels. Default is 1000.
height: Integer. Height of the saved PNG in pixels. Default is 1000.
data: A data frame with row names in the format "nodeA to nodeB", and at minimum two columns: coef (numeric edge weights / standardized coefficients) and p (p-values, used when thresholded = TRUE).
show.color: characer. Color used for outlining significant edges.Default is darkgrey.
thresholded: Logical. If TRUE, edges with p > 0.05 are set to zero (i.e., suppressed in the plot). Default is FALSE.

Value

A ggraph/ggplot2 plot object (invisibly returned via print and return). As a side effect the plot is printed to the active graphics device, and — if filename is provided — written to a 300 dpi PNG file.

Details

Creates a circular network connectogram (chord diagram) from a data frame of connectivity results, visualizing edge weights and their signs using color and transparency. Node self-connections (diagonal elements) are highlighted on the node border. Optionally saves the plot to a PNG file.

Row names of results must follow the pattern "nodeA to nodeB". Self-connections (from == to) are extracted to colour and shade node borders: if all diagonal values are > 1 the border is drawn in hot; if all are < 1 it is drawn in cold. The diagonal entries are removed before the igraph graph object is constructed.

Edge colour encodes sign (hot = positive, cold = negative) and edge transparency encodes absolute magnitude.

The function relies on igraph, ggraph, and ggplot2.

Examples

vizNetConnectogram(colMeans(demomat))