ggmsa (version 0.0.1)

msa_data: msa_data

Description

This function parses FASTA file and convert it to a tidy data frame. The function will also assign color to each molecule (amino acid or nucleotide) according to the selected color scheme. Sequence logo data for drawing alignment label will also be added if font != NULL. The output of msa_data() is the input of geom_msa().

Usage

msa_data(fasta, start = NULL, end = NULL, font = "helvetica_regular",
  color = "Clustal")

Arguments

fasta

Aligned fasta file.

start

Start position to plot,Defaults = NULL.

end

End position to plot, Defaults = NULL.

font

Character font, Defaults is 'helvetica_regular'.

color

A Color scheme. One of 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT', 'Taylor_NT'.Defaults is 'Clustal'.

Value

A data frame

Examples

# NOT RUN {
fasta <- system.file("extdata/sample.fasta", package="ggmsa")
data <- msa_data(fasta, 20, 120, font = 'helvetica_regular', color = 'Chemistry_AA' )
# }