position_site_weblogo: weblogo for specific site of each family

In Busydog1990/genepro: CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences

weblogo for specific site of each family

Description

weblogo for specific site of each family

Usage

position_site_weblogo(
  seqs = NULL,
  alignment_file = NULL,
  group = NULL,
  type = "AA",
  max_seq_length = 30,
  ncol = 1,
  range = "conservation",
  stack_width_threshold = 0.2,
  Specific_site = NULL,
  legend = F,
  stack_width = NULL,
  position_sort = T,
  relative = F,
  mark = F,
  mark_data = NULL,
  title = T,
  title.color = NULL,
  text_angle = 0,
  site_size = 10
)

Arguments

seqs	Aligned sequences.
alignment_file	Path of aligned sequences.
group	Factor. Grouping information of each gene. Must contain the same length of genes.
type	Character. Sequences type, one of DNA, RNA and AA.
max_seq_length	Numeric. The maximum number of site plotted in the weblogo.
ncol	Numeric. The number of columns in Weblogo
range	If range = "conservation", Automatic selection of the most conservative sites.(default) If range = "site", Automatic selection of the most conservative sites from Specific_site data. If class(range) is data.frame, each column in the range represents the locus selected by each family. If class(range) is list, each element in the range represents the locus selected by each family. If is.null(range), first max_seq_length site will be selected by each family. if class(range) is integer/numeric, corresponding site will be selected by each family.
stack_width_threshold	Numeric. Stack width lower than stack_width_threshold will be changed to 0.
Specific_site	Specific_site data. Only available when range = "site"
legend	Logical. If FALSE, legend of weblogo will be deleted. Default: FALSE.
stack_width	Letter width in Weblogo. If is.null(stack_width), the letter width will be calculated automatically according to the conservatism of the locus. If class(stack_width) is data.frame/list, The letter width will be extracted from stack_width. If stack_width is a length 1 numeric/integer vector, width of all letters are set to stack_width. If stack_width is a numeric/integer vector with length > 1. The letter width will be recycled.
position_sort	Logical. If TRUE, position of sites will be sorted. Default: TRUE.
relative	Logical. If FALSE, ylim of weblogo will be fixed.
mark	Logical. If TRUE, Mark on Weblogo. Default: FALSE.
mark_data	Data.frame or List. Only available when mark = TRUE.
title	Logical. If TRUE, title each weblogo.
title.color	The color of title of each weblogo
text_angle	Numeric. Site number angle.Default:0.
site_size	Numeric. Site size.Default:10.

Value

weblogo for specific site of each family.

Busydog1990/genepro documentation built on July 20, 2023, 6:03 a.m.