ggSeqBundle {ggmsa} | R Documentation

## 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)

[Package ggmsa version 1.0.0 Index]