Lineage Plot for top neighbors — lineage.neighbors.plot • MolEvolvR

Lineage plot for top neighbors obtained from DAs of Genomic Contexts.

Usage

lineage.neighbors.plot(
  query_data = "prot",
  query = "pspa",
  colname = "GenContext.norep"
)

query_data: Data frame of protein homologs with the usual 11 columns + additional word columns (0/1 format). Default is pspa_data.
query: Name of query protein/domain. Default is "pspa".
colname: Column name from query_data. Default is "GenContext.norep".

For "da2doms" you would need the file DA.doms.wc as well as the column query_data$DomArch.norep

For "gc2da", you would need the file GC.DA.wc as well as the column query_data$GenContext.norep

Please refer to the source code if you have alternate file formats and/or column names.

Janani Ravi

if (FALSE) { # \dontrun{
lineage.neighbors.plot(pspa_data, pspa, "GenContext.norep", "da2doms")
} # }