as.track.msa: Create an alignment track

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Create an alignment track

Usage

as.track.msa(x, name, refseq = names.msa(x)[1], short.label = NULL,
  pretty = TRUE, nuc.text = NULL, nuc.text.pos = "bottom",
  nuc.text.col = "black")

Arguments

x	An object of type msa
name	The name of the track (a character string)
refseq	A character string identifying the sequence whose coordinate range to use in the plot. A value of NULL implies the frame of reference of the entire alignment.
short.label	An optional character string to be displayed in the left-hand margin of the track
pretty	If TRUE, display bases in the non-reference species which are identical to the reference species as a dot.
nuc.text	If not NULL, can be a vector of character strings. Each character string should be the same length as the MSA with respect to refseq.
nuc.text.pos	If nuc.text is not NULL, can be either "top" or "bottom" to indicate where to place nuc.text relative to the alignment. Will be recycled to the length of nuc.text.
nuc.text.col	If nuc.text is not NULL, color to be used for printing nuc.text. Will be recycled to the length of nuc.text.

Value

An object of type track which can be plotted with the plot.track function

Note

alignment plots will only be displayed if the plot is zoomed in enough to show the alignment data.

Author(s)

Melissa J. Hubisz

See Also

plot.track

rphast documentation built on May 1, 2019, 9:26 p.m.