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Genomic Context Directed Network

Source: R/networks_gencontext.R
createGenomicContextNetwork.Rd

This function creates a Genomic Context network from the 'GenContext' column.

A network of Genomic Context is returned.

Usage

createGenomicContextNetwork(
  prot,
  domains_of_interest,
  column = "GenContext",
  cutoff = 40,
  layout = "grid",
  directed = TRUE
)

Arguments

prot

A data frame that contains the column 'GenContext'.

domains_of_interest

Character vector of domains of interest.

column

Name of column containing Genomic Context from which nodes and edges are generated.

cutoff

Integer. Only use GenContexts that occur at or above the cutoff percentage for total count

layout

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

  • "circle"

  • "random"

  • "auto"

  • "nice"

directed

Is the network directed?

Value

A plot of the genomic context network.

Examples

if (FALSE) { # \dontrun{
gc_directed_network(pspa, column = "GenContext", cutoff = 55)
} # }