ggSeqBundle.Rd
plot Sequence Bundles for MSA based 'ggolot2'
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") )
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"). |
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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 ggalt::geom_xspline(). |
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"). |
ggplot object
Lang Zhou