plot.feat: Features plot

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

Description

plot features

Usage

## S3 method for class 'feat'
plot(x, y = 0, height = 1, plottype = "r",
  arrow.density = 5, angle = 30, col = "black", fill.col = if (plottype
  == "r") col else NULL, lty = par("lty"), lwd = par("lwd"), add = FALSE,
  xlim = range.feat(x), ylim = c(y - height * 3/4, y + height * 3/4), ...)

Arguments

x	an object of type feat
y	the location of the plot on the y axis
height	the height of the boxes
plottype	either "r" for rectangles or "a" for arrows, "b" for arrows within rectangles, or "l" for line segments only.
arrow.density	If plottype=="a" or "b", then this gives the density of arrows in arrows per inch. Otherwise it gives the density of shading lines in the rectangles, and a value of NULL implies no shading lines.
angle	angle (in degrees) of the shading lines or arrows.
col	color to draw the boxes/lines/arrows with.
fill.col	Color to fill the rectangles with. If NULL then do not fill.
lty	line type for lines, arrows, borders, and shading
lwd	line width for lines, arrows, borders and shading
add	if TRUE, add to existing plot
xlim	A numerical vector of length 2 giving the range for the x-axis.
ylim	A numerical vector of length 2 giving the range for the y-axis.
...	graphical parameters to be passed to plot.

Author(s)

Melissa J. Hubisz

Examples

exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
featFile <- "gencode.ENr334-100k.gff"
unzip(exampleArchive, featFile)
f <- read.feat(featFile)
# note that plot(f) does not work because features are stored as data.frames
plot.feat(f[f$feature=="CDS",])
unlink(featFile)

Example output

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