draw.seq {Rgb}

Plot a sequence of nucleotides

Description

This function draws a slice of a character vector, with labels and distinct colors for each nucleotide.

Usage

  draw.seq(slice = NULL, start, end, bty = "o", labelCex = 0.75,
    bases = c(A = "#44CC44", C = "#4444CC", G = "#FFCC00", T = "#CC4444"),
    maxRange = 500, cex.lab = 1, fg = "#000000", ...)

Arguments

slice

Character vector, with a single letter per element.

start

Single integer value, the left boundary of the window, in base pairs.

end

Single integer value, the right boundary of the window, in base pairs.

bty

A character string which determined the type of box which is drawn about plots. If bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box. See par.

labelCex

Single numeric value, character expansion factor for labels.

bases

Named character vector, defining the color to use for each nucleotide (names have to be uppercase, slice is converted to uppercase for matching).

maxRange

Single integer value, nothing will be ploted if the plot window is wider by this value (in bases).

cex.lab

The relative character size of x and y axis labels (default: 1). See par.

fg

Single character value, defining the color of the foreground (axes, labels...) as an english name or a hexadecimal code. Similar to par's argument but not relying on it.

...

Further arguments to be passed to draw.bg.

Author(s)

Sylvain Mareschal

See Also

track.fasta-class

draw.bg, draw.boxes, draw.density, draw.hist, draw.pileup, draw.points, draw.steps