plotDnf: Plot disjunctive normal form.
In mnem: Mixture Nested Effects Models

Description Usage Arguments Value Author(s) Examples

This function visualizes a graph encoded as a disjunctive nromal form.

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,
  ...
)

`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.
`edgelwd`	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.
`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