drawAlignment: Generate a multiple alignment graphic using ggplot

Description Usage Arguments Examples

View source: R/functions.R

Description

Allows the user to plot a multiple alignent using ggplot's grammar of graphics

Usage

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drawAlignment(infile, seqlist, wrap = FALSE, wrap_length = NULL,
  roi = FALSE, roi_data = NULL, consensus = FALSE,
  consensus_height = 5, funct_assoc = FALSE, funct_assoc_data = NULL,
  funct_assoc_height = 5, highlights = FALSE, highlights_data = NULL,
  hlines = FALSE, hlines_data = NULL, ticks = 5,
  ticks_text_size = 30, order = NULL)

Arguments

infile

The multiple alignment to (analyze and) plot.

roi

Plot a subset of the alignment.

consensus

Include in the output graphic a line plot corresponding to the degree of conservation at each site in the alignment.

funct_assoc

Include in the output graphic a line plot of the association between AA residues and

Examples

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LucasBusta/phyloChemistry documentation built on Dec. 19, 2018, 12:15 a.m.