Description Usage Arguments Value Examples
This function builds a data frame to plot an alignment from a specified subset of the full alignment.
1 2 | extract_subalign(seqs, plot_step = 1, tlist = c(), clist = c(),
texcl = FALSE, cexcl = FALSE)
|
seqs |
Sequence list, as parsed by the function 'read_alignment' |
plot_step |
Step size for alignment block. Default, 1. |
tlist |
Array of taxa intended to restrict figure to or to exclude from figure. |
clist |
Array of columns intended to restrict figure to or to exclude from figure. |
texcl |
Boolean indicating if taxa in tlist should be excluded. Default, False |
cexcl |
Boolean indicating if columns in clist should be excluded. Default, False |
plot_frame, a data frame to be plotted
1 2 3 4 | fasta_file <- system.file("extdata", "example.fasta", package = "alignfigR")
plot_frame <- read_alignment(file = fasta_file)
subset_seq_list <- extract_subalign(plot_frame, tlist = c("Cow", "Human", "Whale"), texcl = TRUE)
subset_seq_list <- extract_subalign(plot_frame, clist = 1:25)
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