snha_layout {snha} | R Documentation |
Determine graph layouts
Description
This function returns xy coordinates for a given input adjacency matrix or snha graph. It is useful if you like to plot the same set of nodes with different edge connections in the same layout.
Usage
snha_layout(
A,
mode='sam',
method='pearson',
noise=FALSE,
star.center=NULL,
interactive=FALSE)
Arguments
A |
an adjacency matrix or an snha graph object |
mode |
character string for the layout type, can be either 'mds' (mds on graph using shortest paths), 'mdsd' (mds on data) 'sam' (sammon on graph), 'samd' (sammon on data), 'circle', 'grid' or 'star', default: 'sam' |
method |
method for calculating correlation distance if mode is either 'mdsd' or 'samd', default: 'pearson' |
noise |
should some noise be added, default: FALSE |
star.center |
the centered node if layout is 'star', must be a character string for the node name, default: NULL |
interactive |
switch into interactive mode where you can click in the graph and move nodes with two clicks, first selecting the node, second click gives the new coordinates for the node, default: FALSE |
Value
matrix with x and y columns for the layout
Examples
data(swiss)
sw.s=snha(swiss,method='spearman')
sw.p=snha(swiss,method='pearson')
lay=snha_layout(sw.s,mode='sam')
plot(sw.s,layout=lay)
plot(sw.p,layout=lay)
plot(sw.s,layout='star',star.center='Education')
rn1=rnorm(nrow(swiss))
nswiss=cbind(swiss,Rn1=rn1)
plot(snha(nswiss,method='spearman'),layout='sam')
plot(snha(nswiss,method='spearman'),layout='samd',
vertex.size=2,vertex.color='beige')