plotDnf {mnem} | R Documentation |
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 |
Rgraphviz object
Martin Pirkl
g <- c("!A+B+C=G", "C=G", "!D=G") plotDnf(g)