createUndirectedGenomicContextNetwork

This function creates a domain network from the 'DomArch' column.

A network of domains is returned based on shared domain architectures.

Usage

createUndirectedGenomicContextNetwork(
  prot,
  column = "GenContext",
  domains_of_interest,
  cutoff_type = "Lineage",
  cutoff = 1,
  layout = "grid"
)

Arguments

prot

A data frame that contains the column 'DomArch'.

column

Name of column containing Domain architecture from which nodes and edges are generated.

domains_of_interest

Character vector specifying the domains of interest.

cutoff_type

Character. Used to determine how data should be filtered. Either

• "Total Count" to filter off the total amount of times a domain architecture occurs

cutoff

Integer. Only use domains that occur at or above the cutoff for total counts if cutoff_type is "Total Count". Only use domains that appear in cutoff or greater lineages if cutoff_type is Lineage.

layout

Character. Layout type to be used for the network. Options are:

• "circle"

• "random"

• "auto"

Value

A plot of the domain architecture network.

Examples

if (FALSE) { # \dontrun{
createUndirectedGenomicContextNetwork(pspa, column = "DomArch", 
domains_of_interest = c("Domain1", "Domain2"), 
cutoff_type = "Total Count", cutoff = 10)
} # }