plotIPR2Viz

plotIPR2Viz

Usage

plotIPR2Viz(
  infile_ipr = NULL,
  infile_full = NULL,
  accessions = c(),
  analysis = c("Pfam", "Phobius", "TMHMM", "Gene3D"),
  group_by = "Analysis",
  topn = 20,
  name = "Name",
  text_size = 15,
  query = "All"
)

Arguments

infile_ipr

A path to the input IPR file (TSV format) containing domain information.

infile_full

A path to the full input file (TSV format) containing lineage and accession information.

accessions

A character vector of accession numbers to filter the analysis. Default is an empty vector.

analysis

A character vector specifying the types of analysis to include (e.g., "Pfam", "Phobius", "TMHMM", "Gene3D"). Default is a vector of these analyses.

group_by

A string specifying how to group the visualization. Default is "Analysis". Options include "Analysis" or "Query".

topn

An integer specifying the number of top accessions to visualize. Default is 20.

name

A string representing the name to use for y-axis labels. Default is "Name".

text_size

An integer specifying the text size for the plot. Default is 15.

query

A string for filtering a specific query name. If it is not "All", only the data matching this query will be processed.

Value

A ggplot object representing the domain architecture visualization.

Examples

if (FALSE) { # \dontrun{
plot <- plotIPR2Viz(infile_ipr = "path/to/ipr_file.tsv",
                    infile_full = "path/to/full_file.tsv",
                    accessions = c("ACC123", "ACC456"),
                    analysis = c("Pfam", "TMHMM"),
                    group_by = "Analysis",
                    topn = 20,
                    name = "Gene Name",
                    text_size = 15,
                    query = "All")
plot
} # }