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

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

Usage

createDomainNetwork(
  prot,
  column = "DomArch",
  domains_of_interest,
  cutoff = 70,
  layout = "nice",
  query_color = adjustcolor("green", alpha.f = 0.5)
)

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 domains of interest.

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

Character. Color to represent the queried domain in the network.

Value

A network visualization of domain architectures.

Examples

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