draw.bg: Background for track plots

In Rgb: The R Genome Browser

Background for track plots

Description

This function draws the background for the other track ploting functions.

Usage

  draw.bg(start, end, ylab = "", ylab.horiz = FALSE, ysub = as.character(NA),
    mar = c(0.2, 5, 0.2, 1), xaxt = "s", yaxt = "n", yaxs = "r", ylim = c(0, 1),
    cex.lab = 1, cex.axis = 1, mgp = c(3, 1, 0), tck = NA, tcl = -0.5,
    xaxp = as.numeric(NA), yaxp = as.numeric(NA), bty = "o", las = 0, xgrid = TRUE,
    new = FALSE, bg = NA, bg.inner = NA, fg = "#000000", ...)

Arguments

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.
ylab	The name of the Y axis. See par.
ylab.horiz	Single logical value, whether to print ylab horizontally or not.
ysub	Similar to ylab, but written on a closer line when yaxt is "n". Can be NA to disable it.
mar	A numerical vector of the form "c(bottom, left, top, right)" which gives the number of lines of margin to be specified on the four sides of the plot. See par.
xaxt	Whether to plot an X axis ("s") or not ("n"). See par.
yaxt	Whether to plot an Y axis ("s") or not ("n"). If no Y axis is drawn, ysub may be used to plot a sub-title to the Y axis. See par.
yaxs	Y axis style, "r" enlarges the Y limits by 4 percents on each side for a cleaner look, "i" will not. See par.
ylim	The Y axis limits as a numerical vector of the form "c(start, end)" of the plot. Note that start > end is allowed and leads to a "reversed axis". Use "NULL" to guess the axis range from the data. See plot.default.
cex.lab	The relative character size of x and y axis labels (default: 1). See par.
cex.axis	The relative character size of x and y axis annotations (default: 1). See par.
mgp	Length 3 vector defining the distance between the plot area and respectively the Y axis label, Y axis annotations and Y axis line (default: 3, 1, 0). See par.
tck	The length of tick marks as a fraction of the smaller of the width or height of the plot (default: NA, meaning using tcl instead). See par.
tcl	The absolute length of a tick marks. Note that positive numbers put them inside the plot area (default: -0.5). See par.
xaxp	Length 3 vector defining the ticks on the X axis : X of first tick, X of last tick and number of intervals between them (default: NA). See par.
yaxp	Length 3 vector defining the ticks on the Y axis : Y of first tick, Y of last tick and number of intervals between them (default: NA). See par.
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.
las	The direction of both X and Y axis labels: 0 for labels parallel to the axes, 1 for horizontal labels, 2 for labels perpendicular to the axes and 3 for vertical labels. See par.
xgrid	Single logical value, whether to draw a grid on X axis or not.
new	Single logical value, whether to plot on top of previous track (TRUE) or in a new track (FALSE, default).
bg	Single character value, defining the color of the background (margins included) as an english name or a hexadecimal code. Similar to par's argument but not relying on it, NA corresponds to the default par-based behavior.
bg.inner	Single character value, defining the color of the background (margins excluded) as an english name or a hexadecimal code. NA corresponds to the default par-based behavior.
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.
...	Not used, only ignores other arguments.

Author(s)

Sylvain Mareschal

See Also

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

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.