drawGraph: Drawing a graph with a simple point and click interface.

In ggm: Graphical Markov Models with Mixed Graphs

Description

Draw a graph from its adjacency matrix representation.

Usage

drawGraph(amat, coor = NULL, adjust = FALSE, alpha = 1.5,
                beta = 3, lwd = 1, ecol = "blue", bda = 0.1, layout = layout.auto)

Arguments

amat	the adjacency matrix representation of the graph. This can be an undirected graph, a directed acyclic graph or a mixed graph with at most a summary graph structure. See also plotGraph

.

coor	an optional matrix of dimensions p x 2 where p is the number of vertices of the graph. If coor=NULL then the function chooses a default position for the nodes.
adjust	a logical value, defaults to FALSE. If TRUE the graph is plotted and the system waits until the mouse button is pressed (same behaviour of locator function.
alpha	a positive value between controlling the distance from the end of the edges to the nodes of the graph.
beta	a positive value controlling the distance of the labels of the variables from the nodes.
lwd	line width of the edges (default: 1).
ecol	color of the edges (default: "blue").
bda	bidirected edge arrow length (default: 0.1).
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 adjust is TRUE.

Details

The function is a very simple tool useful for displaying small graphs, with a rudimentary interface for moving nodes and edges of a given graph and adjusting the final plot. For better displays use dynamicGraph or Rgraphviz package in Bioconductor project.

Value

The function plots the graph with a initial positioning of the nodes, as specified by coor and remains in a waiting state. The position of each node can be shifted by pointing and clicking (with the first mouse button) close to the node. When the mouse button is pressed the node which is closer to the selected point is moved to that position. Thus, one must be careful to click closer to the selected node than to any other node. The nodes can be moved to any position by repeating the previous operation. The adjustment process is terminated by pressing any mouse button other than the first.

At the end of the process, the function returns invisibly the coordinates of the nodes. The coordinates may be used later to redisplay the graph.

Author(s)

Giovanni M. Marchetti

References

dynamicGraph, Rgraphwiz, http://www.bioconductor.org.

GraphViz, Graph Visualization Project. AT\&T Research. http://www.graphviz.org.

See Also

UG, DAG, makeMG, plotGraph

Examples

## A directed acyclic graph
d <- DAG(y1 ~ y2+y6, y2 ~ y3, y3 ~ y5+y6, y4 ~ y5+y6)
## Not run: drawGraph(d)

## An undirected graph
g <- UG(~giova*anto*armo + anto*arj*sara) 
## Not run: drawGraph(d)

## An ancestral graph
ag <- makeMG(ug=UG(~y0*y1), dg=DAG(y4~y2, y2~y1), bg=UG(~y2*y3+y3*y4))
drawGraph(ag, adjust = FALSE)
drawGraph(ag, adjust = FALSE)

## A more complex example with coordinates: the UNIX evolution
xy <-
structure(c(5, 15, 23, 25, 26, 17, 8, 6, 6, 7, 39, 33, 23, 49, 
19, 34, 13, 29, 50, 68, 70, 86, 89, 64, 81, 45, 64, 49, 64, 87, 
65, 65, 44, 37, 64, 68, 73, 85, 83, 95, 84, 0, 7, 15, 27, 44, 
37, 36, 20, 51, 65, 44, 64, 59, 73, 69, 78, 81, 90, 97, 89, 72, 
85, 74, 62, 68, 59, 52, 48, 43, 50, 34, 21, 18, 5, 1, 10, 2, 
11, 2, 1, 44), .Dim = c(41, 2), .Dimnames = list(NULL, c("x", 
"y")))
Unix <- DAG(
                SystemV.3 ~ SystemV.2,
                SystemV.2 ~ SystemV.0,
                SystemV.0 ~ TS4.0,
                TS4.0 ~ Unix.TS3.0 + Unix.TS.PP + CB.Unix.3,
                PDP11.SysV ~ CB.Unix.3,
                CB.Unix.3 ~ CB.Unix.2,
                CB.Unix.2 ~ CB.Unix.1,
                Unix.TS.PP ~ CB.Unix.3,
                Unix.TS3.0 ~ Unix.TS1.0 + PWB2.0 + USG3.0 + Interdata,
                USG3.0 ~ USG2.0,
                PWB2.0 ~ Interdata + PWB1.2,
                USG2.0 ~ USG1.0,
                CB.Unix.1 ~ USG1.0,
                PWB1.2 ~ PWB1.0,
                USG1.0 ~ PWB1.0,
                PWB1.0 ~ FifthEd,
                SixthEd ~ FifthEd,
                LSX ~ SixthEd,
                MiniUnix ~ SixthEd,
                Interdata ~ SixthEd,
                Wollongong ~ SixthEd,
                SeventhEd ~ Interdata,
                BSD1 ~ SixthEd,
                Xenix ~ SeventhEd,
                V32 ~ SeventhEd,
                Uniplus ~ SeventhEd,
                BSD3 ~ V32,
                BSD2 ~ BSD1,
                BSD4 ~ BSD3,
                BSD4.1 ~ BSD4,
                EigthEd ~ SeventhEd + BSD4.1,
                NinethEd ~ EigthEd,
                Ultrix32 ~ BSD4.2,
                BSD4.2 ~ BSD4.1,
                BSD4.3 ~ BSD4.2,
                BSD2.8 ~ BSD4.1 + BSD2,
                BSD2.9 ~ BSD2.8,
                Ultrix11 ~ BSD2.8 + V7M + SeventhEd,
                V7M ~ SeventhEd
                )
drawGraph(Unix, coor=xy, adjust=FALSE)
# dev.print(file="unix.fig", device=xfig) # Edit the graph with Xfig

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'ggm'

The following object is masked from 'package:igraph':

    pa

ggm documentation built on March 26, 2020, 7:49 p.m.