plotDnf {mnem} | R Documentation

## Plot disjunctive normal form.

### Description

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

### 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.
`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

### Value

Rgraphviz object

### Author(s)

Martin Pirkl

### Examples

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

[Package mnem version 1.10.0 Index]