snha (version 0.1.3)

plot.snha: display network or correlation matrices of snha graphs

Description

The function `plot.snha` provides a simple display of network graphs correlation matrices using filled circles (vertices) to represent variables and edges which connect the vertices with high absolute. correlation values. Positive correlations are shown in black, negative correlations are shown in red. For more information see the details section.

Usage

# S3 method for snha
plot( 
 x, 
 type = "network", 
 layout = "circle", 
 vertex.color = "salmon", 
 cex = 1, 
 vertex.size = 5, 
 edge.width = 2, 
 edge.color = c("grey70", "red"), 
 edge.text = NULL, 
 edge.cex = 0.8, 
 edge.pch = 0, 
 noise = FALSE, 
 hilight.chain = NULL, 
 chain.color = c("black", "red"), 
 star.center = NULL, 
 plot.labels = TRUE, 
 lty = 1, 
 threshold = c(0.25, 0.5, 0.75), 
 interactive = FALSE, 
 ... 
)

Value

returns the layout of the plotted network or NULL if type is `corrplot` (invisible)

Arguments

x

snha graph object usually created with the 'snha' function or an adjacency matrix

type

character string specifying the plot type either 'network' or ' cor', default: 'network'

layout

graph layout for plotting one of 'circle', 'sam', 'samd', 'grid', 'mds', 'mdsd', 'star', default: 'circle'

vertex.color

default color for the vertices, either a single value, all vertices have hen this color or a vector of values, for different colors for the nodes, default: 'salmon'

cex

size of the vertex labels which are plotted on the vertices, default: 1

vertex.size

number how large the vertices should be plotted, default: 5

edge.width

number on how strong the edges should be plotted, if edge.width=0, then the number is based on the correlation values, default: 2

edge.color

color to be plotted for edges. Usually vector of length two. First color for positive correlations, second color for negative correlations. Default: c('grey','red')

edge.text

optional matrix to give edge labels, default: NULL

edge.cex

character expansion for edge labels, default: 0.8

edge.pch

plotting character which should be placed below the edge.text, default: 0

noise

should be noise added to the layout. Sometimes useful if nodes are too close. Default: FALSE

hilight.chain

which chain should be highlighted, default: NULL (no chain highlight)

chain.color

which color for chain edges, default: black

star.center

the centered node if layout is 'start', must be a character string for the node name, default: NULL

plot.labels

should node labels plotted, default: TRUE

lty

line type for standard edges in the graph, default: 1

threshold

cutoff values for bootstrap probabilities for drawing edges as dotted, broken lines and solid lines, default: c(0.25,0.5,0.75)

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

...

currently not used

Details

This is a plot function to display networks or correlation matrices of 'snha' graph objects. In case of bootstrapping the graph by using the `snha` function with the `prob=TRUE` option lines in style full, broken and dotted lines are drawn if they are found in more than 75, 50 or 25 percent of all re-samplings. You can change these limits by using the `threshold` argument.

Examples

data(swiss) 
sw.g=snha(swiss,method='spearman') 
sw.g$theta 
round(sw.g$sigma,2) 
plot(sw.g,type='network',layout='circle') 
plot(sw.g,type='network',layout='sam') 
plot(sw.g,type='corplot') 
# adding correlation values 
plot(sw.g,edge.text=round(sw.g$sigma,2),edge.cex=1.2,edge.pch=15) 
sw.g=snha(swiss,method='spearman',prob=TRUE) 
sw.g$theta 
sw.g$probabilities 
plot(sw.g,type='network',layout='sam') 
sw.g$chains 
# plot chains for a node 
plot(sw.g,layout="sam",lty=2,hilight.chain="Infant.Mortality", 
 edge.width=3,edge.color=c("black","red")) 
# an example for an adjacency matrix 
M=matrix(rbinom(100,1, 0.2),nrow=10,ncol=10) 
diag(M)=0 
colnames(M)=rownames(M)=LETTERS[1:10] 
plot.snha(M)