Printing Sequence Alignments
Print method for fasta and pdbs sequence alignment objects.
## S3 method for class 'fasta'
print(x, alignment=TRUE, ...)
.print.fasta.ali(x, width = NULL, col.inds = NULL, numbers = TRUE,
conservation=TRUE, ...)x |
a sequence alignment object as obtained from the functions
|
alignment |
logical, if TRUE the sequence alignment will be printed to screen. |
width |
a single numeric value giving the number of residues per printed sequence block. By default this is determined from considering alignment identifier widths given a standard 85 column terminal window. |
col.inds |
an optional numeric vector that can be used to select subsets of alignment positions/columns for printing. |
numbers |
logical, if TRUE position numbers and a tick-mark every 10 positions are printed above and below sequence blocks. |
conservation |
logical, if TRUE conserved and semi-conserved columns in the alignment are marked with an ‘*’ and ‘^’, respectively. |
... |
additional arguments to ‘.print.fasta.ali’. |
Called mostly for its effect but also silently returns block divided concatenated sequence strings as a matrix.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
file <- system.file("examples/kif1a.fa",package="bio3d")
aln <- read.fasta(file)
print(aln)
# print(aln, col.inds=30:100, numbers=FALSE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.