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
createBinaryDomainNetwork(
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.
- domains_of_interest
Character vector specifying the 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
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
- border_color
Color for the borders of the nodes.
- IsDirected
Is the network directed? Set to false to eliminate arrows