plotDnf: Plot disjunctive normal form.

In cbg-ethz/mnem: Mixture Nested Effects Models

Plot disjunctive normal form.

Description

This function visualizes a graph encoded as a disjunctive nromal form. See the graphviz documentation for possible input arguments, like edgehead/tail: https://graphviz.org/docs/attr-types/arrowType/

Usage

plotDnf(
  dnf = NULL,
  freq = NULL,
  stimuli = c(),
  signals = c(),
  inhibitors = c(),
  connected = TRUE,
  CNOlist = NULL,
  cex = NULL,
  fontsize = NULL,
  labelsize = NULL,
  type = 2,
  lwd = 1,
  edgelwd = 1,
  legend = 0,
  x = 0,
  y = 0,
  xjust = 0,
  yjust = 0,
  width = 1,
  height = 1,
  layout = "dot",
  main = "",
  sub = "",
  cex.main = 1.5,
  cex.sub = 1,
  col.sub = "grey",
  fontcolor = NULL,
  nodestates = NULL,
  simulate = NULL,
  edgecol = NULL,
  labels = NULL,
  labelcol = "blue",
  nodelabel = NULL,
  nodecol = NULL,
  bordercol = NULL,
  nodeshape = NULL,
  verbose = FALSE,
  edgestyle = NULL,
  nodeheight = NULL,
  nodewidth = NULL,
  edgewidth = NULL,
  lty = NULL,
  hierarchy = NULL,
  showall = FALSE,
  edgehead = NULL,
  edgelabel = NULL,
  edgetail = NULL,
  bool = TRUE,
  draw = TRUE,
  ...
)

Arguments

dnf	Hyper-graph in disjunctive normal form, e.g. c("A=B", "A=C+D", "E=!B") with the child on the left and the parents on the right of the equation with "A=C+D" for A = C AND D. Alternatively, dnf can be an adjacency matrix, which is converted on the fly to a disjunctive normal form.
freq	Frequency of hyper-edges which are placed on the edges.
stimuli	Highlights vertices which can be stimulated.
signals	Highlights vertices which regulate E-genes.
inhibitors	Highlights vertices which can be inhibited.
connected	If TRUE, only includes vertices which are connected to other vertices.
CNOlist	CNOlist object. Optional instead of stimuli, inhibitors or signals. See package CellNOptR.
cex	Global font size.
fontsize	Vertice label size.
labelsize	Edge label size.
type	Different plot types. 2 for Rgraphviz and 1 for graph.
lwd	Line width of nodeborder.
edgelwd	Global edgeline width.
legend	0 shows no legend. 1 shows legend as a graph. 2 shows legend in a standard box.
x	x coordinate of box legend.
y	y coordinate of box legend.
xjust	Justification of legend box left, right or center (-1,1,0).
yjust	Justification of legend box top, bottom or middle (-1,1,0).
width	Vertice width.
height	Vertice height.
layout	Graph layout. See graphvizCapabilities()$layoutTypes.
main	Main title.
sub	Subtitle.
cex.main	Main title font size.
cex.sub	Subtitle font size.
col.sub	Font color of subtitle.
fontcolor	Global font color.
nodestates	Binary state of each vertice.
simulate	Simulate stimulation and inhibition of a list of vertices. E.g. simulate = list(stimuli = c("A", "B"), inhibitors = c("C", "D")).
edgecol	Vector with colors for every edge of the graph (not hyper-graph). E.g. an AND gate consists of three distinct edges.
labels	Vector with labels for the edges.
labelcol	Vector with label colors for the edges.
nodelabel	List of vertices with labels as input. E.g. labels = list(A="test", B="label for B").
nodecol	List of vertices with colors as input.
bordercol	List of vertices with colors as input.
nodeshape	List of vertices with shapes (diamond, box, square,...).
verbose	Verbose output.
edgestyle	set the edge style like dashed, can be numerical
nodeheight	List of vertices with height as input.
nodewidth	List of vertices with width as input.
edgewidth	Vector with edge widths for individual edges.
lty	Vector with edge styles (line, dotted,...).
hierarchy	List with the hierarchy of the vertices. E.g. list(top = c("A", "B"), bottom = c("C", "D")).
showall	See "connected" above.
edgehead	Vector with edge heads.
edgelabel	Vector with edge labels.
edgetail	Vector with edge tails.
bool	If TRUE, only shows normal graph and no AND gates.
draw	Do not plot the graph and only output the graphNEL object.
...	additional arguments

Value

Rgraphviz object

Author(s)

Martin Pirkl

Examples

g <- c("!A+B+C=G", "C=G", "!D=G")
plotDnf(g)

cbg-ethz/mnem documentation built on Nov. 7, 2024, 7:35 p.m.