visualize_MSA_using_ggmsa: A function to quickly visualize the alignment generated by...

In currocam/taxa2hmmer: Get more out of homologous sequence search with HMMER

A function to quickly visualize the alignment generated by HMMER using ggmsa.

Description

A function to quickly visualize the alignment generated by HMMER using ggmsa.

Usage

visualize_MSA_using_ggmsa(
  msa,
  start = NULL,
  end = NULL,
  color_scheme = "Chemistry_AA",
  max_positions_per_row = NULL,
  alignment_index = NULL,
  format = "fasta"
)

Arguments

msa	An AAMultipleAlignment, an AAStringSet or a character vector of one with the file path of a fasta file. In case of using a file, take into account the format argument.
start	A numeric vector of one. Start position to plot.
end	A numeric vector of one. End position to plot.
color_scheme	A character vector of one. Frequently used values are: 'Clustal', 'Chemistry_AA', 'Shapely_AA', 'Zappo_AA', 'Taylor_AA', 'LETTER', 'CN6', 'Chemistry_NT', 'Shapely_NT', 'Zappo_NT' or 'Taylor_NT'.
max_positions_per_row	A numeric vector of one. Maximum number of positions in each row
alignment_index	A numeric vector with the desired sequences to plot or a vector of characters with their names. We recommend no more than 15.
format	A character vector of one. The format of the alignment file, if used.

Value

An aplot. It can be modified using the rest of the ggmsa library functions.

currocam/taxa2hmmer documentation built on April 10, 2022, 11:02 a.m.