plotG {gRapHD} | R Documentation |
Plots a graph using the Fruchterman-Reingold algorithm.
plotG(model=NULL,edges=NULL,v=NULL,numIter=50,main=NULL,tcex=1, plotVert=TRUE,labelVert=TRUE,energy=FALSE, useWeights=FALSE,hlv=NULL,hlc="red",vs=0.01, pos=NULL,edcol="darkgray",edlty=1,edlwd=1,vlcol=0, sb=1,lcex=.40,vlabs=NULL,asp=NA,disp=TRUE,font=1)
model |
a gRapHD object. |
edges |
matrix with 2 columns, each row representing one edge, and each column one of the vertices in the edge. |
v |
list of vertices to be plotted. If NULL , all vertices will be
plotted |
numIter |
number of iterations for the Fruchterman-Reingold algorithm. |
main |
main title. |
tcex |
numeric character expansion factor for the main title; multiplied
by par yields the final character
size. NULL and NA are equivalent to 1.0 . |
plotVert |
if TRUE the vertices are plotted. |
labelVert |
if TRUE the vertices are labelled. |
energy |
if TRUE use the minimum energy as initial values. |
useWeights |
if TRUE use the model$statSeq as edge length
weights). |
hlv |
list of vertices to be highlighted. |
hlc |
colour to be used in the highlighted vertices. |
vs |
radii of the edges (scalar or vector with length equal to the number of vertices). See 'Details'. |
pos |
initial coordinate values for the vertices. |
edcol |
colour of the edges. |
edlty |
type of line for the edges. |
edlwd |
width of the line for the edges. |
vlcol |
colour of the vertices borders. |
sb |
symbol to be used in the vertices (length 1 or number of vertices):
0 is a ellipse (a=2*vs ,b=vs ), 1 a circle, 2 a square,
3 or higher represents the number of sides. |
lcex |
numeric character expansion factor for the labels; multiplied by
par yields the final character size.
NULL and NA are equivalent to 1.0 . |
vlabs |
labels to be used in the vertices. If NULL , the vertices
numbers are used. |
asp |
numeric, giving the aspect ratio y/x
(see plot.window for more details). |
disp |
if TRUE (default), the graph is plotted. |
font |
an integer which specifies which font to use for the labels. If possible, device drivers let 1 correspond to plain text (the default), 2 to bold face, 3 to italic and 4 to bold italic. |
Plot a graph based on the list of edges.
Only one (model
or edges
) should be provided. If model
,
the function uses also the information about the type of variables (discrete
or continuous). If edges
, then all variables are plotted as continuous
(circles).
The plotting area is square, ranging from 0 to 1. The unit of parameter
vs
follow the axes.
The algorithm proposed by Fruchterman & Reingold (1991) is used to determine
the position of each vertex. It is not initialised randomly, but in a regular
grid.
If ret
is TRUE
, the coordinates for the vertices are returned.
Gabriel Coelho Goncalves de Abreu (Gabriel.Abreu@agrsci.dk)
Rodrigo Labouriau (Rodrigo.Labouriau@agrsci.dk)
David Edwards (David.Edwards@agrsci.dk)
Fruchterman, T.M.J. and Reingold, E.M. (1991) Graph Drawing by Force-directed
Placement. SOFTWARE-PRACTICE AND EXPERIENCE, VOL. 21(11), 1129-1164.
Csardi G, Nepusz T: The igraph software package for complex network
research, InterJournal, Complex Systems 1695. 2006.
http://igraph.sf.net
data(dsCont) m1 <- minForest(dsCont,homog=TRUE,forbEdges=NULL,stat="LR") plotG(model=m1,numIter=1000) # or plotG(edges=m1$edges,numIter=1000) # or plotG(edges=m1$edges,v=c(13,28,32,10,16,26,31,22),numIter=1000) # or plotG(edges=m1$edges,v=1:40,numIter=1000) # or plotG(model=m1,numIter=1000,plotVert=FALSE,labelVert=FALSE) ############# r <- 3 edges <- rep(1,r) x <- 2+r-1 edges <- c(edges,sort(rep(2:x,r-1))) edges <- c(edges,sort(rep((x+1):(x+(x-1)*(r-1)),r-2))) edges <- c(edges,sort(rep((x+(x-1)*(r-1)+1):(x+(x-1)*(r-1)+(x-1)*(r-1)*(r-2)),r-3))) edges <- cbind(edges,2:(length(edges)+1)) a <- neighbourhood(edges=edges,orig=1,rad=r) vs <- a$v[,2] vs <- 1/vs vs[1] <- 2 vs <- vs/30 plotG(edges=edges,numIter=200,hlv=a$v[,1],hlc=colours()[386:383][a$v[,2]+1],vs=vs)