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

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

Usage

plotLineageDA(
  query_data = "prot",
  colname = "DomArch",
  cutoff = 90,
  RowsCutoff = FALSE,
  color = "default"
)

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".
cutoff: Numeric. Cutoff for word frequency. Default is 90.
RowsCutoff: Boolean. If TRUE, applies a row cutoff to remove data rows based on a certain condition. Default is FALSE.
color: Color for the heatmap. One of six options: "default", "magma", "inferno", "plasma", "viridis", or "cividis"

A LineageDA plot object.

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{
plotLineageDA(toast_rack_data, 10, "DomArch.norep", "da2doms")
} # }