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Domain Network

Source: R/networks_domarch.R
BinaryDomainNetwork.Rd

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

Domains that are part of the 'domains_of_interest' are a different node color than the other domains.

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

Usage

BinaryDomainNetwork(
  prot,
  column = "DomArch",
  domains_of_interest,
  cutoff = 70,
  layout = "nice",
  query_color = adjustcolor("yellow", alpha.f = 0.5),
  partner_color = adjustcolor("skyblue", alpha.f = 0.5),
  border_color = adjustcolor("grey", alpha.f = 0.8),
  IsDirected = T
)

Arguments

prot

A data frame that contains the column 'DomArch'.

column

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

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"

query_color

Color that the nodes of the domains in the domains_of_interest vector are colored

partner_color

Color that the nodes that are not part of the domains_of_interest vector are colored

IsDirected

Is the network directed? Set to false to eliminate arrows

Examples

if (FALSE) { # \dontrun{
domain_network(pspa)
} # }