TikzCode: Generate Tikz Code for Plot

In rje42/DAGtools: Tools for fitting and analysing DAGs via MCMC

Generate Tikz Code for Plot

Description

Generate Tikz Code for Plot

Usage

TikzCode(
  x,
  file = "",
  z,
  n_pos,
  bend,
  ud_thresh = 0.5,
  cutoff = 0.1,
  func,
  bend_double = TRUE,
  rev = FALSE,
  col = c("black", "black", "blue", "red"),
  labels = NULL,
  nodesOnTop = TRUE,
  edgeScale = 1,
  ...
)

Arguments

x	adjacency matrix from MCMC summary
file	file to output code (defaults to stout)
z	optionally, a matrix of z-scores
n_pos	optional matrix of node positions (requires Rgraphviz if not specified)
bend	edge angles
ud_thresh	threshold for drawing edges as undirected
cutoff	threshold for including edges
func	vectorized function to transform probabilities
bend_double	bend automatically if arrows in two different directions?
rev	logical - should thickness and density plotting be reversed?
col	colours for undirected, directed and positive and negative edges
labels	character vector of labels for nodes
nodesOnTop	logical: should nodes be on top of everything else
edgeScale	scales edges to a desired width
...	other arguments

Details

If more than ud_thresh of the edges present are in a particular direction, then the two directions are drawn separately, otherwise an undirected edge is drawn. Edges present in less than cutoff sampled graphs are ignored entirely. func is a transformation that can be applied to the probability (e.g. squaring it to reduce the visual impact of weak edges). This must take a matrix and return a matrix of the transformed values.

If z is specified, then the function will plot the thickness of the line to be related to this quantity. If rev = TRUE then the thickness of the line is related to the size of the effect, and the density of colour to the proportion of samples containing that effect.

col is given as a character vector of up to four colours. The order is undirected positive and negative, followed by directed positive and negative. Colours are just repeated if necessary.

If labels is not provided these are taken from the rownames of x.

rje42/DAGtools documentation built on June 6, 2024, 3:13 a.m.