ggSeqBundle: ggSeqBundle

In YuLab-SMU/ggmsa: Plot Multiple Sequence Alignment using 'ggplot2'

ggSeqBundle

Description

plot Sequence Bundles for MSA based 'ggolot2'

Usage

ggSeqBundle(
  msa,
  line_widch = 0.3,
  line_thickness = 0.3,
  line_high = 0,
  spline_shape = 0.3,
  size = 0.5,
  alpha = 0.2,
  bundle_color = c("#2ba0f5", "#424242"),
  lev_molecule = c("-", "A", "V", "L", "I", "P", "F", "W", "M", "G", "S", "T", "C",
    "Y", "N", "Q", "D", "E", "K", "R", "H")
)

Arguments

msa	Multiple sequence alignment file(FASTA) or object for representing either nucleotide sequences or peptide sequences.Also receives multiple MSA files. eg:msa = c("Gram-negative_AKL.fasta", "Gram-positive_AKL.fasta").
line_widch	The width of bundles at each site, default is 0.3.
line_thickness	The thickness of bundles at each site, default is 0.3.
line_high	The high of bundles at each site, default is 0.
spline_shape	A numeric vector of values between -1 and 1, which control the shape of the spline relative to the control points. From geom_xspline() in ggalt package.
size	A numeric vector of values between o and 1, which control the size of each lines.
alpha	A numeric vector of values between o and 1, which control the alpha of each lines.
bundle_color	The colors of each sequence bundles. eg: bundle_color = c("#2ba0f5","#424242").
lev_molecule	Reassigning the Y-axis and displaying letter-coded amino acids/nucleotides arranged by physiochemical properties or others.eg:amino acids hydrophobicity lev_molecule = c("-","A", "V", "L", "I", "P", "F", "W", "M", "G", "S","T", "C", "Y", "N", "Q", "D", "E", "K","R", "H").

Value

ggplot object

Author(s)

Lang Zhou

Examples

aln <- system.file("extdata", "Gram-negative_AKL.fasta", package = "ggmsa")
ggSeqBundle(aln)

YuLab-SMU/ggmsa documentation built on Dec. 18, 2024, 11:53 p.m.