combi_p: combi_p

In BioVizSeq: Visualizing the Elements Within Bio-Sequences

combi_p

Description

Get ggplot2 files to facilitate free combination in patchwork

Usage

combi_p(
  tree_path,
  gff_path = NULL,
  meme_path = NULL,
  pfam_path = NULL,
  cdd_path = NULL,
  fa_path = NULL,
  smart_path = FALSE,
  plantcare_path = NULL,
  promoter_length = NULL,
  renamefile = NULL,
  groupfile = NULL,
  shape = "RoundRect",
  r = 0.3,
  legend_size = 6
)

Arguments

tree_path	The path of tree file (.newick).
gff_path	The path of .gff/gtf file.
meme_path	The path of .meme/mast file.
pfam_path	The path of pfam result file (.tsv).
cdd_path	The path of cdd result file (.txt).
fa_path	The path of protein file (.fa/fasta).
smart_path	Do SMART or not. (TRUE or FALSE)
plantcare_path	The path of plantcare file (.tab).
promoter_length	The length of promoter.
renamefile	Rename file. Two cols: new_name and old_name.
groupfile	Group information. Two cols: label and Group.
shape	RoundRect or Rect.
r	The radius of rounded corners.
legend_size	The size of legend.

Value

list

Author(s)

Shiqi Zhao

Examples

tree_path <- system.file("extdata", "idpep.nwk", package = "BioVizSeq")
plot_file <- combi_p(tree_path)

BioVizSeq documentation built on Aug. 22, 2025, 9:13 a.m.