legend2: A legend which allows longer lines
In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description Usage Arguments Details Value Author(s) References See Also Examples

This function can be used to add legends to plots. This is almost identical to the legend function, accept it has an extra parameter, seg.len which allows the user to change the lengths of lines shown in legends.

legend2(x, y = NULL, legend, fill = NULL, col = par("col"), 
    lty, lwd, pch, angle = 45, density = NULL, bty = "o", bg = par("bg"), 
    box.lwd = par("lwd"), box.lty = par("lty"), pt.bg = NA, cex = 1, 
    pt.cex = cex, pt.lwd = lwd, xjust = 0, yjust = 1, x.intersp = 1, 
    y.intersp = 1, adj = c(0, 0.5), text.width = NULL, text.col = par("col"), 
    merge = do.lines && has.pch, trace = FALSE, plot = TRUE, 
    ncol = 1, horiz = FALSE, title = NULL, inset = 0, seg.len = 2)

`x, y`	the x and y co-ordinates to be used to position the legend. They can be specified by keyword or in any way which is accepted by `xy.coords`: See Details.
`legend`	a character or expression vector. of length >= 1 to appear in the legend. Other objects will be coerced by `as.graphicsAnnot`.
`fill`	if specified, this argument will cause boxes filled with the specified colors (or shaded in the specified colors) to appear beside the legend text.
`col`	the color of points or lines appearing in the legend.
`lty, lwd`	the line types and widths for lines appearing in the legend. One of these two must be specified for line drawing.
`pch`	the plotting symbols appearing in the legend, either as vector of 1-character strings, or one (multi character) string. Must be specified for symbol drawing.
`angle`	angle of shading lines.
`density`	the density of shading lines, if numeric and positive. If `NULL` or negative or `NA` color filling is assumed.
`bty`	the type of box to be drawn around the legend. The allowed values are `"o"` (the default) and `"n"`.
`bg`	the background color for the legend box. (Note that this is only used if `bty != "n"`.)
`box.lty, box.lwd`	the line type and width for the legend box.
`pt.bg`	the background color for the `points`, corresponding to its argument `bg`.
`cex`	character expansion factor relative to current `par("cex")`.
`pt.cex`	expansion factor(s) for the points.
`pt.lwd`	line width for the points, defaults to the one for lines, or if that is not set, to `par("lwd")`.
`xjust`	how the legend is to be justified relative to the legend x location. A value of 0 means left justified, 0.5 means centered and 1 means right justified.
`yjust`	the same as `xjust` for the legend y location.
`x.intersp`	character interspacing factor for horizontal (x) spacing.
`y.intersp`	the same for vertical (y) line distances.
`adj`	numeric of length 1 or 2; the string adjustment for legend text. Useful for y-adjustment when `labels` are plotmath expressions.
`text.width`	the width of the legend text in x (`"user"`) coordinates. (Should be positive even for a reversed x axis.) Defaults to the proper value computed by `strwidth(legend)`.
`text.col`	the color used for the legend text.
`merge`	logical; if `TRUE`, “merge” points and lines but not filled boxes. Defaults to `TRUE` if there are points and lines.
`trace`	logical; if `TRUE`, shows how `legend` does all its magical computations.
`plot`	logical. If `FALSE`, nothing is plotted but the sizes are returned.
`ncol`	the number of columns in which to set the legend items (default is 1, a vertical legend).
`horiz`	logical; if `TRUE`, set the legend horizontally rather than vertically (specifying `horiz` overrides the `ncol` specification).
`title`	a character string or length-one expression giving a title to be placed at the top of the legend. Other objects will be coerced by `as.graphicsAnnot`.
`inset`	inset distance(s) from the margins as a fraction of the plot region when legend is placed by keyword.
`seg.len`	numeric specifying length of lines in legend.

Arguments x, y, legend are interpreted in a non-standard way to allow the coordinates to be specified via one or two arguments. If legend is missing and y is not numeric, it is assumed that the second argument is intended to be legend and that the first argument specifies the coordinates.

The coordinates can be specified in any way which is accepted by xy.coords. If this gives the coordinates of one point, it is used as the top-left coordinate of the rectangle containing the legend. If it gives the coordinates of two points, these specify opposite corners of the rectangle (either pair of corners, in any order).

The location may also be specified by setting x to a single keyword from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". This places the legend on the inside of the plot frame at the given location. Partial argument matching is used. The optional inset argument specifies how far the legend is inset from the plot margins. If a single value is given, it is used for both margins; if two values are given, the first is used for x- distance, the second for y-distance.

“Attribute” arguments such as col, pch, lty, etc, are recycled if necessary. merge is not.

Points are drawn after lines in order that they can cover the line with their background color pt.bg, if applicable.

See the examples for how to right-justify labels.

A list with list components

rect

a list with components

w, h: positive numbers giving width and height of the legend's box.
left, top: x and y coordinates of upper left corner of the box.

text

a list with components

x, y: numeric vectors of length length(legend), giving the x and y coordinates of the legend's text(s).

returned invisibly.

Richard Pearson (modified from original graphics package function.)

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth \& Brooks/Cole.

Murrell, P. (2005) R Graphics. Chapman & Hall/CRC Press.

legend

if(FALSE){
x <- seq(-pi, pi, len = 65)
plot(x, sin(x), type = "l", ylim = c(-1.2, 1.8), col = 3, lty = 2)
points(x, cos(x), pch = 3, col = 4)
lines(x, tan(x), type = "b", lty = 1, pch = 4, col = 6)
title("legend(..., lty = c(2, -1, 1), pch = c(-1,3,4), merge = TRUE)",
      cex.main = 1.1)
legend2(-1, 1.9, c("sin", "cos", "tan"), col = c(3,4,6),
       text.col = "green4", lty = c(2, -1, 1), pch = c(-1, 3, 4),
       merge = TRUE, bg = 'gray90', seg.len=6)
}