single.network: Plot a network given a threshold

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

This function plots a network connecting nodes showing distances equal or lower than the defined threshold value.

Usage

single.network(dis, threshold = NA, ptPDF = TRUE, ptPDFname = "Network.pdf",
bgcol = "white", label.col = "black", label = colnames(dis), modules = FALSE,
moduleCol = NA, modFileName = "Modules_summary.txt", na.rm.row.col = FALSE,

cex.vertex = 1, plot = TRUE, get.coord = FALSE, refer2max = TRUE

)

Arguments

dis	the distance matrix to be represented
threshold	a numeric between 0 and 1, is the value of the maximum distance to be considered as a link. This value is referred to the maximum distance in the input matrix (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 32% of the maximum distance found in the distance matrix).
ptPDF	a logical, must the percolation network be saved as a pdf file?
ptPDFname	if ptPDF=TRUE, the name of the pdf file containing the percolation network to be saved ("percolationNetwork.pdf", by default)
bgcol	string defining the colour of the background for each node in the network. Can be equal for all nodes (if only one colour is defined), customized (if several colours are defined), or can represent different modules (see modules option).
label.col	vector of strings defining the colour of labels for each node in the network. Can be equal for all nodes (if only one colour is defined) or customized (if several colours are defined).
label	vector of strings, labels for each node. By default are the column names of the distance matrix (dis). (See substr function in base package to automatically reduce name lengths).
modules	a logical, must nodes belonging to different modules be represented as different colours?
moduleCol	(if modules=TRUE) vector of strings, defining the colour of nodes belonging to different modules in the network.
modFileName	(if modules=TRUE) the name of a generated file containing a summary of module results
na.rm.row.col	a logical; if TRUE, missing values are removed before the computation proceeds.
cex.vertex	a numeric, the size of vertex
plot	a logical, TRUE to plot the inferred network
get.coord	a logical, TRUE to obtain coordinates of nodes within the network
refer2max	a logic, "TRUE" to refer the threshold value to the maximum distance in the input matrix (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 32% of the maximum distance found in the distance matrix). "FALSE" to refer the threshold to a specific value (e.g., a value of 0.32 will represent a link between nodes showing distances equal or lower than 0.32, regardless the maximum distance found in the distance matrix).

Author(s)

A. J. Muñoz-Pajares

See Also

perc.thr, NINA.thr

Examples

#generating distance matrix:
dis<-matrix(nrow=12,c(0.0000,0.5000,0.1875,0.5000,0.6250,0.5000,0.2500,0.6250,
0.3750,0.3750,0.3750,0.3750,0.5000,0.0000,0.7500,0.0000,0.6250,0.0000,0.8750,
0.6250,0.3750,0.3750,0.3750,0.3750,0.1875,0.7500,0.0000,0.7500,0.8750,0.7500,
0.2500,0.8750,0.6250,0.6250,0.6250,0.6250,0.5000,0.0000,0.7500,0.0000,0.6250,
0.0000,0.8750,0.6250,0.3750,0.3750,0.3750,0.3750,0.6250,0.6250,0.8750,0.6250,
0.0000,0.6250,0.5000,0.0000,0.2500,0.2500,0.2500,0.2500,0.5000,0.0000,0.7500,
0.0000,0.6250,0.0000,0.8750,0.6250,0.3750,0.3750,0.3750,0.3750,0.2500,0.8750,
0.2500,0.8750,0.5000,0.8750,0.0000,0.5000,0.5000,0.5000,0.5000,0.5000,0.6250,
0.6250,0.8750,0.6250,0.0000,0.6250,0.5000,0.0000,0.2500,0.2500,0.2500,0.2500,
0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,0.0000,0.0000,
0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,0.0000,
0.0000,0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,0.0000,
0.0000,0.0000,0.0000,0.3750,0.3750,0.6250,0.3750,0.2500,0.3750,0.5000,0.2500,
0.0000,0.0000,0.0000,0.0000))
row.names(dis)<-c("Population1_sequence1","Population1_sequence2",
"Population1_sequence3","Population1_sequence4","Population2_sequence1",
"Population2_sequence2","Population2_sequence3","Population2_sequence4",
"Population3_sequence1","Population3_sequence2","Population3_sequence3",
"Population3_sequence4")
colnames(dis)<-row.names(dis)

#Representing distances equal or lower than 37% of the maximum distance:
# single.network(dis=dis,threshold=0.37,label=paste(substr(row.names(dis),11,11),
# substr(row.names(dis),21,21),sep="-"))

sidier documentation built on June 25, 2021, 5:10 p.m.