drawAlignment: Generate a multiple alignment graphic using ggplot

In thebustalab/phylochemistry: Chemical and Sequence Analyses in a Phylogenetic Context

Description

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

Usage

drawAlignment(
  infile,
  seqlist,
  alignment_labels,
  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,
  tick_spacing = 5,
  ticks_text_size = 30,
  order = NULL,
  color_pal = NULL
)

Arguments

infile	The alignment to use (fasta file)
seqlist	A dataframe with metadata for the alignment
alignment_labels	The name of the column to label the entries in the alignment with
wrap	TRUE/FALSE whether to use a column of plots to show the alignment
wrap_length	Length at which to cut the wrap
roi	TRUE/FALSE whether to only show regions of interest in the alignment
roi_data	Dataframe defining the regions to show
consensus	TRUE/FALSE whether to include a consensus line in the alignment
consensus_height	Height of the consensus line plot
funct_assoc	TRUE/FALSE whether to show functional associations in the alignment
funct_assoc_data	Columns in the metadata dataframe to use in searching for functional association (e.g. "c(sterol~other, sterol~cyclo)")
funct_assoc_height	Height of the functional association lines
highlights	TRUE/FALSE whether to highlight certain sites in the alignment
highlights_data	Dataframe specifying which site to highlight
hlines	TRUE/FALSE whether to divide the alignment with horizontal lines
hlines_data	Dataframe specifying where to divide alignment
tick_spacing	Spacing between x-axis ticks
ticks_text_size	Size of x-axis ticks text
order	Order in which to display the members of the alignment
color_pal	Color palette to use

Examples

drawAlignment()

thebustalab/phylochemistry documentation built on Sept. 3, 2021, 5:06 a.m.