NEArender (version 1.5)

connectivity: Connectivity

Description

Function for plotting node degree distribution in order to test if the network is scale-free

Usage

connectivity(NET, Lowercase = 1, col.1 = 1, col.2 = 2, col.score = 3,
  echo = 1, main = "Connectivity plot", min.score = NA, n.top = NA,
  hex = FALSE)

Arguments

NET

Input network file.

Lowercase

If node IDs should be rendered lower-case (Default:1, i.e. 'yes').

col.1

Number of column where 1st node of each edge should be found (only needed when NET is a text file rather than a list).

col.2

Number of column where 2nd node of each edge should be found (only needed when NET is a text file rather than a list, i.e. passed down to import.net).

col.score

Number of column where edge confidence score is found (only needed when NET is a text file rather than a list, i.e. passed down to import.net).

echo

If messages about execution progress should appear.

main

title name for the plot, default: "Connectivity plot"

min.score

Minimum confidence score for an edge to be included in the network (is alternative to n.top and is only used when NET is a text file rather than a list, i.e. passed down to import.net).

n.top

Number of edges to be included in the network, top when ranked by confidence score (is alternative to min.score and only used when NET is a text file rather than a list, i.e. passed down to import.net).

hex

If the node degree distribution should be presented as density plot using package hexbin.

See Also

benchmark and import.net

Examples

# NOT RUN {
file <-  system.file("extdata", "Connectivity.FC1_full", package = "NEArender")
# }
# NOT RUN {
connect <- connectivity(file,hex=TRUE)
# }