plotGraph: Plot of a mixed graph

In ggm: Graphical Markov Models with Mixed Graphs

Plot of a mixed graph

Description

Plots a mixed graph from an adjacency matrix, a graphNEL object, an igraph object, or a descriptive vector.

Usage

plotGraph(a, dashed = FALSE, tcltk = TRUE, layout = layout.auto,
directed = FALSE, noframe = FALSE, nodesize = 15, vld = 0, vc = "gray",
vfc = "black", colbid = "FireBrick3", coloth = "black", cex = 1.5, ...)

Arguments

a	An adjacency matrix: a matrix that consists of 4 different integers as an ij-element: 0 for a missing edge between i and j, 1 for an arrow from i to j, 10 for a full line between i and j, and 100 for a bi-directed arrow between i and j. These numbers can be added to generate multiple edges of different types. The matrix must be symmetric w.r.t full lines and bi-directed arrows. Or a graph that can be a graphNEL or an igraph object.Or a vector of length 3e, where e is the number of edges of the graph, that is a sequence of triples (type,node1label,node2label). The type of edge can be "a" (arrows from node1 to node2), "b" (arcs), and "l" (lines).
dashed	A logical value. If TRUE the bi-directed edges are plotted as undirected dashed edges.
tcltk	A logical value. If TRUE the function opens a tcltk device to plot the graphs, allowing the interactive manimulation of the graph. If FALSEthe function opens a standard device without interaction.
layout	The name of a function used to compute the (initial) layout of the graph. The default is layout.auto. This can be further adjusted if tcltk is TRUE.
directed	A logical value. If FALSE a symmetric adjacency matrix with entries 1 is interpreted as an undirected graph. If TRUE it is interpreted as a directed graph with double arrows. If a is not an adjacency matrix, it is ignored.
noframe	A logical value. If TRUE, then the nodes are not circled.
nodesize	An integer denoting the size of the nodes (default 15). It can be increased to accommodate larger labels.
vld	An integer defining the distance between a vertex and its label. Defaults to 0.
vc	Vertex color. Default is "gray".
vfc	Vertex frame color. Default is "black".
colbid	Color of the bi-directed edges. Default is "FireBrick3".
coloth	Color of all the other edges. Default is "black".
cex	An integer (defaults to 1) to adjust the scaling of the font of the labels.
...	Further arguments to be passed to plot or tkplot.

Details

plotGraph uses plot and tkplot in igraph package.

Value

Plot of the associated graph and returns invisibly a list with two slots: tkp.id, graph, the input graph as an igraph object. The id can be used to get the layout of the adjusted graph. The bi-directed edges are plotted in red.

Author(s)

Kayvan Sadeghi, Giovanni M. Marchetti

See Also

grMAT, tkplot, drawGraph, plot.igraph

Examples

exvec<-c("b",1,2,"b",1,14,"a",9,8,"l",9,11,
         "a",10,8,"a",11,2,"a",11,9,"a",11,10,
         "a",12,1,"b",12,14,"a",13,10,"a",13,12)
plotGraph(exvec)
############################################
amat<-matrix(c(0,11,0,0,10,0,100,0,0,100,0,1,0,0,1,0),4,4)
plotGraph(amat)
plotGraph(makeMG(bg = UG(~a*b*c+ c*d), dg = DAG(a ~ x + z, b ~ z )))
plotGraph(makeMG(bg = UG(~a*b*c+ c*d), dg = DAG(a ~ x + z, b ~ z )), dashed = TRUE)
# A graph with double and triple edges
G <-
structure(c(0, 101, 0, 0, 100, 0, 100, 100, 0, 100, 0, 100, 0,
111, 100, 0), .Dim = c(4L, 4L), .Dimnames = list(c("X", "Z",
"Y", "W"), c("X", "Z", "Y", "W")))
plotGraph(G)
# A regression chain graph with longer labels
 plotGraph(makeMG(bg = UG(~Love*Constraints+ Constraints*Reversal+ Abuse*Distress),
   dg = DAG(Love ~ Abuse + Distress, Constraints ~ Distress, Reversal ~ Distress,
   Abuse ~ Fstatus, Distress ~ Fstatus),
   ug = UG(~Fstatus*Schooling+ Schooling*Age)),
   dashed = TRUE, noframe = TRUE)
# A graph with 4 edges between two nodes.
G4 = matrix(0, 2, 2); G4[1,2] = 111; G4[2,1] = 111
plotGraph(G4)

ggm documentation built on May 29, 2024, 7:27 a.m.