Lineage Plot for top neighbors — plotLineageNeighbors • MolEvolvR

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

Usage

plotLineageNeighbors(
  query_data = "prot",
  query = "pspa",
  colname = "GenContext.norep"
)

Arguments

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".

Value

A ggplot object representing a heatmap (tile plot) of lineage versus the top neighboring domain architectures, with color intensity representing the frequency of occurrences.

Details

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

Note

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

Author

Janani Ravi

Examples

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