legend.HazardShape: Customize legend for `plot.HazardShape` outputs

Description

Put legend after run plot.HazardShape function.

Usage

legend.HazardShape(
  x,
  y = NULL,
  legend = c("Empirical TTT", "Spline curve"),
  fill = NULL,
  col = 1,
  border = "white",
  lty = NA,
  lwd = NA,
  pch = c(1, NA),
  angle = 45,
  density = NULL,
  bty = "o",
  bg = par("bg"),
  box.lwd = par("lwd"),
  box.lty = par("lty"),
  box.col = par("fg"),
  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"),
  text.font = NULL,
  merge = TRUE,
  trace = FALSE,
  plot = TRUE,
  ncol = 1,
  horiz = FALSE,
  title = NULL,
  inset = 0,
  xpd = TRUE,
  title.col = text.col[1],
  title.adj = 0.5,
  title.cex = cex[1],
  title.font = text.font[1],
  seg.len = 2,
  curve_options = list(col = 2, lwd = 2, lty = 1)
)

Arguments

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 \(\ge 1\) 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.
border: the border color for the boxes (used only if fill is specified).
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, as numeric vector or a vector of 1-character strings (see points). Unlike points, this can all be specified as a single 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, box.col: the line type, width and color for the legend box (if bty = "o").
pt.bg: the background color for the points, corresponding to its argument bg.
cex: character expansion factor relative to current par("cex"). Used for text, and provides the default for pt.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 between symbol and legend text.
y.intersp: vertical (y) distances (in lines of text shared above/below each legend entry). A vector with one element for each row of the legend can be used.
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.) Can be a single positive numeric value (same width for each column of the legend), a vector (one element for each column of the legend), NULL (default) for computing a proper maximum value of strwidth(legend)), or NA for computing a proper column wise maximum value of strwidth(legend)).
text.col: the color used for the legend text.
text.font: the font used for the legend text, see 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.
xpd: if supplied, a value of the graphical parameter xpd to be used while the legend is being drawn.
title.col: color for title, defaults to text.col[1].
title.adj: horizontal adjustment for title: see the help for par("adj").
title.cex: expansion factor(s) for the title, defaults to cex[1].
title.font: the font used for the legend title, defaults to text.font[1], see text.
seg.len: the length of lines drawn to illustrate lty and/or lwd (in units of character widths).
curve_options: a list whose names are curve graphical parameters, and whose values are the corresponding graphical parameters values.

Author

Jaime Mosquera Gutiérrez jmosquerag@unal.edu.co

Details

This function is a wrapper for the legend function. It just adds two features:

legend has a default value, regarding that HazardShape objects produces the TTT plot and its LOESS estimation.
curve_options is used to set legend parameters for the LOESS curve. We encourage you to define first a list with curve parameters, and then pass it to plot.HazardShape and legend.HazardShape (see example 2).

Examples

Run this code

library(EstimationTools)

data("reduction_cells")
TTT_IG <- TTTE_Analytical(Surv(days, status) ~ 1, data = reduction_cells,
                          method = 'censored')
HS_IG <- TTT_hazard_shape(TTT_IG, data = reduction_cells)

#----------------------------------------------------------------------------
# Example 1: put legend to the TTT plot of the reduction cells data set.

# Run `plot.HazardShape` method.
par(
  cex.lab=1.8,
  cex.axis=1.8,
  mar=c(4.8,5.4,1,1),
  las = 1,
  mgp=c(3.4,1,0)
)
plot(HS_IG, pch = 16, cex = 1.8)

# Finally, put the legend
legend.HazardShape(
  x = "bottomright",
  box.lwd = NA,
  cex = 1.8,
  pt.cex = 1.8,
  bty = 'n',
  pch = c(16, NA)
)
#----------------------------------------------------------------------------
# Example 2: example 1 with custom options for the curve

# This is the list with curve parameters
loess_options <- list(
  col = 3, lwd = 4, lty = 2
)
par(
  cex.lab=1.8,
  cex.axis=1.8,
  mar=c(4.8,5.4,1,1),
  las = 1,
  mgp=c(3.4,1,0)
)

plot(HS_IG, pch = 16, cex = 1.8, curve_options = loess_options)
legend.HazardShape(
  x = "bottomright",
  box.lwd = NA,
  cex = 1.8,
  pt.cex = 1.8,
  bty = 'n',
  pch = c(16, NA),
  curve_options = loess_options
)

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