Lineage Plot: Heatmap of Domains/DAs/GCs vs Lineages

Lineage plot for Domains, Domain Architectures and Genomic Contexts. Heatmap.

Usage

lineage.DA.plot(
  query_data = "prot",
  colname = "DomArch",
  cutoff = 90,
  RowsCutoff = FALSE,
  color = "default"
)

Arguments

query_data

Data frame of protein homologs with the usual 11 columns + additional word columns (0/1 format). Default is prot (variable w/ protein data).

colname

Column name from query_data: "DomArch.norep", "GenContext.norep", "DomArch.PFAM.norep" or "DomArch.LADB.norep". Default is "DomArch.norep".

color

Color for the heatmap. One of six options: "default", "magma", "inferno", "plasma", "viridis", or "cividis"

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{
lineage.DA.plot(toast_rack_data, 10, "DomArch.norep", "da2doms")
} # }