as.track.feat: Create a features track

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

Description

Create a features track

Usage

as.track.feat(x, name, short.label = NULL, col = "black", is.gene = FALSE,
  arrow.density = 10)

Arguments

x	An object of type feat
name	The name of the track (a character string)
short.label	An optional character string to be displayed in left hand margin of track
col	The color to use plotting this track (can be a single color or a color for each element)
is.gene	A logical value; if TRUE, extract and plot gene information from features. The features which will be plotted are the ones with types "CDS", "exon", or "intron". All others will be ignored.
arrow.density	(Only used if is.gene==TRUE. The number of lines per inch used to denote strand in gene plots.

Value

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

Author(s)

Melissa J. Hubisz

Examples

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "sol1.gp"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
featTrack <- as.track.feat(f, "basic feature track")
f <- add.introns.feat(f)
geneTrack <- as.track.feat(f, "gene track", is.gene=TRUE)
plot.track(list(featTrack, geneTrack))
plot.track(list(featTrack, geneTrack, geneTrack, geneTrack, geneTrack),
           xlim=c(14800, 16000))
unlink(featFile)

Example output

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