R: Methods for Function plot in Package 'RobAStBase'

plot-methods {RobAStBase}

R Documentation

Methods for Function plot in Package ‘RobAStBase’

Description

plot-methods

Usage

plot(x, y, ...)
## S4 method for signature 'IC,missing'
plot(x, ..., withSweave = getdistrOption("withSweave"),
             main = FALSE, inner = TRUE, sub = FALSE,
             col.inner = par("col.main"), cex.inner = 0.8,
             bmar = par("mar")[1], tmar = par("mar")[3],
             with.automatic.grid = TRUE,
             with.legend = FALSE, legend = NULL, legend.bg = "white",
             legend.location = "bottomright", legend.cex = 0.8,
             withMBR = FALSE, MBRB = NA, MBR.fac = 2, col.MBR = par("col"),
             lty.MBR = "dashed", lwd.MBR = 0.8,
             x.vec = NULL, scaleX = FALSE, scaleX.fct, scaleX.inv,
             scaleY = FALSE, scaleY.fct = pnorm, scaleY.inv=qnorm,
             scaleN = 9, x.ticks = NULL, y.ticks = NULL,
             mfColRow = TRUE, to.draw.arg = NULL,
             withSubst = TRUE)
## S4 method for signature 'IC,numeric'
plot(x, y, ...,
                 cex.pts = 1, cex.pts.fun = NULL, col.pts = par("col"),
                 pch.pts = 19,
                 cex.npts = 1, cex.npts.fun = NULL, col.npts = par("col"),
                 pch.npts = 20,
                 jitter.fac = 1, with.lab = FALSE, cex.lbs = 1, adj.lbs = c(0,0),
                 col.lbs = col.pts, lab.pts = NULL, lab.font = NULL,
                 alpha.trsp = NA, which.lbs = NULL,
                 which.Order = NULL, which.nonlbs = NULL, attr.pre = FALSE,
                 return.Order = FALSE)

Arguments

`x`	object of class `"IC"`: IC to be plotted
`y`	missing or numeric (a dataset, e.g.)
`withSweave`	logical: if `TRUE` (for working with `Sweave`) no extra device is opened
`main`	logical: is a main title to be used? or just as argument `main` in `plot.default`.
`inner`	logical: do panels have their own titles? or character vector of inner titles/ cast to length 'number of plotted dimensions'; if argument `to.draw.arg` is used, this refers to a vector of length `length(to.draw.arg)`, the actually plotted dimensions. For further information, see also description of argument `main` in `plot.default`.
`sub`	logical: is a sub-title to be used? or just as argument `sub` in `plot.default`.
`tmar`	top margin – useful for non-standard main title sizes
`bmar`	bottom margin – useful for non-standard sub title sizes
`cex.inner`	magnification to be used for inner titles relative to the current setting of `cex`; as in `par`
`col.inner`	character or integer code; color for the inner title
`with.automatic.grid`	logical; should a grid be plotted alongside with the ticks of the axes, automatically? If `TRUE` a respective call to `grid` in argument `panel.first` is ignored.
`with.legend`	logical; shall a legend be plotted?
`legend`	either `NULL` or a list of length (number of plotted panels) of items which can be used as argument `legend` in command `legend`.
`legend.location`	a valid argument `x` for `legend` — the place where to put the legend on the last issued plot — or a list of length (number of plotted panels) of such arguments, one for each plotted panel.
`legend.bg`	background color for the legend
`legend.cex`	magnification factor for the legend
`withMBR`	logical; shall horizontal lines with min and max of MBRE be plotted for comparison?
`MBRB`	matrix (or `NA`); coerced by usual recycling rules to a matrix with as many rows as plotted panels and with first column the lower bounds and the second column the upper bounds for the respective coordinates (ideally given by the MBR-IC).
`MBR.fac`	positive factor; scales the bounds given by argument `MBRB`
`col.MBR`	color for the MBR lines; as usual `col`-argument;
`lty.MBR`	line type for the MBR lines; as usual `lty`-argument;
`lwd.MBR`	line width for the MBR lines; as usual `lwd`-argument;
`x.vec`	a numeric vector of grid points to evaluate the influence curve; by default, `x.vec` is `NULL`; then the grid is produced automatically according to the distribution of the IC. `x.vec` can be useful for usage with a rescaling of the x-axis to avoid that the evaluation points be selected too unevenly (i.e. on an equally spaced grid in the original scale, but then, after rescaling non-equally). The grid has to be specified in original scale; i.e.; when used with rescaling, it should be chosen non-equally spaced.
`scaleX`	logical; shall X-axis be rescaled (by default according to the cdf of the underlying distribution)?
`scaleY`	logical; shall Y-axis be rescaled (by default according to a probit scale)?
`scaleX.fct`	an isotone, vectorized function mapping the domain of the IC to [0,1]; if `scaleX` is `TRUE` and `scaleX.fct` is missing, the cdf of the underlying observation distribution; can also be a list of functions with one list element for each of the panels to be plot.
`scaleX.inv`	the inverse function to `scale.fct`, i.e., an isotone, vectorized function mapping [0,1] to the domain of the IC such that for any `x` in the domain, `scaleX.inv(scaleX.fct(x))==x`; if `scaleX` is `TRUE` and `scaleX.inv` is missing, the quantile function of the underlying observation distribution; can also be a list of functions with one list element for each of the panels to be plot.
`scaleY.fct`	an isotone, vectorized function mapping for each coordinate the range of the respective coordinate of the IC to [0,1]; defaulting to the cdf of `{\cal N}(0,1)`.
`scaleY.inv`	an isotone, vectorized function mapping for each coordinate the range [0,1] into the range of the respective coordinate of the IC; defaulting to the quantile function of `{\cal N}(0,1)`.
`scaleN`	integer; defaults to 9; on rescaled axes, number of x and y ticks if drawn automatically;
`x.ticks`	numeric; defaults to NULL; (then ticks are chosen automatically); if non-NULL, user-given x-ticks (on original scale);
`y.ticks`	numeric; defaults to NULL; (then ticks are chosen automatically); if non-NULL, user-given y-ticks (on original scale); can be a list with one (numeric or NULL) item per panel
`mfColRow`	shall default partition in panels be used — defaults to `TRUE`
`to.draw.arg`	Either `NULL` (default; everything is plotted) or a vector of either integers (the indices of the subplots to be drawn) or characters — the names of the subplots to be drawn: these names are to be chosen either among the row names of the trafo matrix `rownames(trafo(eval(x@CallL2Fam)@param))` or if the last expression is `NULL` a vector `"dim<dimnr>"`, `dimnr` running through the number of rows of the trafo matrix.
`withSubst`	logical; if `TRUE` (default) pattern substitution for titles and lables is used; otherwise no substitution is used.
`cex.pts`	size of the points of the second argument plotted, can be a vector; if argument `attr.pre` is `TRUE`, it is recycled to the length of all observations and determines the sizes of all plotted symbols, i.e., the selection is done within this argument; in this case argument `col.npts` is ignored. If `attr.pre` is `FALSE`, `cex.pts` is recycled to the number of the observations selected for labelling and refers to the index ordering after the selection. Then argument `cex.npts` deteremines the sizes of the shown but non-labelled observations as given in argument `which.nonlbs`.
`cex.pts.fun`	rescaling function for the size of the points to be plotted; either `NULL` (default), then `log(1+abs(x))` is used for each of the rescalings, or a function which is then used for each of the rescalings, or a list of functions; if it is a function or a list of functions, if necessary it is recylced to length `dim` where `dim` is the number of dimensions of the pICs to be plotted.
`col.pts`	color of the points of the second argument plotted, can be a vector as in `cex.pts` (with `col.npts` as counterpart).
`pch.pts`	symbol of the points of the second argument plotted, can be a vector as in `cex.pts` (with `pch.npts` as counterpart).
`col.npts`	color of the non-labelled points of the `data` argument plotted; (may be a vector).
`pch.npts`	symbol of the non-labelled points of the `data` argument plotted (may be a vector).
`cex.npts`	size of the non-labelled points of the `data` argument plotted (may be a vector).
`cex.npts.fun`	rescaling function for the size of the non-labelled points to be plotted; either `NULL` (default), then `log(1+abs(x))` is used for each of the rescalings, or a function which is then used for each of the rescalings, or a list of functions; if it is a function or a list of functions, if necessary it is recylced to length `dim` where `dim` is the number of dimensions of the pICs to be plotted.
`with.lab`	logical; shall labels be plotted to the observations?
`cex.lbs`	size of the labels; can be vectorized to a matrix of dim nlbs x npnl where npnl is the number of plotted panels and nlbs the number of plotted labels; if it is a vector, it is recylced in order label then panel.
`col.lbs`	color of the labels; can be vectorized as `col.pts`.
`adj.lbs`	adjustment of the labels; can be vectorized to a 2 x npnl matrix, npnl the number of plotted panels; if it is a vector, it is recycled in order (x,y)-coords then panel.
`lab.pts`	character or NULL; labels to be plotted to the observations; if `NULL` observation indices;
`lab.font`	font to be used for labels (of the observations).
`alpha.trsp`	alpha transparency to be added ex post to colors `col.pch` and `col.lbl`; if one-dim and NA all colors are left unchanged. Otherwise, with usual recycling rules `alpha.trsp` gets shorted/prolongated to length the data-symbols to be plotted. Coordinates of this vector `alpha.trsp` with NA are left unchanged, while for the remaining ones, the alpha channel in rgb space is set to the respective coordinate value of `alpha.trsp`. The non-NA entries must be integers in [0,255] (0 invisible, 255 opaque).
`jitter.fac`	jittering factor used in case of a `DiscreteDistribution` for plotting points of the second argument in a jittered fashion.
`attr.pre`	logical; do graphical attributes for plotted data refer to indices prior (`TRUE`) or posterior to selection via arguments `which.lbs`, `which.Order`, `which.nonlbs` (`FALSE`)?
`which.lbs`	either an integer vector with the indices of the observations to be plotted into graph or `NULL` — then no observation is excluded
`which.Order`	we order the observations (descending) according to the norm given by `normtype(object)`; then `which.Order` either is an integer vector with the indices of the ordered observations (remaining after a possible reduction by argument `which.lbs`) to be plotted (with labels) into graph or `NULL` — then no (further) observation is excluded.
`which.nonlbs`	indices of the observations which should be plotted but not labelled; either an integer vector with the indices of the observations to be plotted into graph or `NULL` — then all non-labelled observations are plotted
`return.Order`	logical; if `TRUE`, an order vector is returned; more specifically, the order of the (remaining) observations given by their original index is returned (remaining means: after a possible reduction by argument `which.lbs`, and ordering is according to the norm given by `normtype(object)`); otherwise we return `invisible()` as usual.
`...`	further parameters for `plot`

Details

Any parameters of plot.default may be passed on to this particular plot method.

We start describing the IC,missing-method: For main-, inner, and subtitles given as arguments main, inner, and sub, top and bottom margins are enlarged to 5 resp. 6 by default but may also be specified by tmar / bmar arguments. If main / inner / sub are logical then if the respective argument is FALSE nothing is done/plotted, but if it is TRUE, we use a default main title taking up the calling arguments in case of main, default inner titles taking up the class and (named) parameter slots of arguments in case of inner, and a "generated on <data>"-tag in case of sub. Of course, if main / inner / sub are character, this is used for the title; in case of inner it is then checked whether it has correct length. If argument withSubst is TRUE, in all title and axis lable arguments, the following patterns are substituted:

"%C": class of argument object
"%A": deparsed argument object
"%D": time/date-string when the plot was generated

If argument ... contains argument ylim, this may either be as in plot.default (i.e. a vector of length 2) or a vector of length 2*(number of plotted dimensions + 2), where the first two elements are the values for ylim in panel "d", the first two are for ylim resp. xlim for panels "p" and "q", and the last 2*(number of plotted dimensions) are the values for ylim for the plotted dimensions of the L2derivative, one pair for each dimension.

The IC,numeric-method calls the IC,missing-method but in addition plots the values of a dataset into the IC.

In addition, argument ... may contain arguments panel.first, panel.last, i.e., hook expressions to be evaluated at the very beginning and at the very end of each panel (within the then valid coordinates). To be able to use these hooks for each panel individually, they may also be lists of expressions (of the same length as the number of panels and run through in the same order as the panels).

Value

An S3 object of class c("plotInfo","DiagnInfo"), i.e., a list containing the information needed to produce the respective plot, which at a later stage could be used by different graphic engines (like, e.g. ggplot) to produce the plot in a different framework. A more detailed description will follow in a subsequent version.

Examples

IC1 <- new("IC")
plot(IC1)
plot(IC1, main = TRUE, panel.first= grid(),
     col = "blue", cex.main = 2, cex.inner = 1)

### selection of subpanels for plotting
N <- NormLocationScaleFamily(mean=0, sd=1) 
IC2 <- optIC(model = N, risk = asCov())
par(mfrow=c(1,1))
plot(IC2, main = TRUE, panel.first= grid(),
     col = "blue", cex.main = 2, cex.inner = 0.6,
     mfColRow = FALSE, to.draw.arg=c("sd"))

## xlim and ylim arguments
plot(IC2, main = TRUE, panel.first= grid(), 
     ylim=c(-3,3), xlim=c(-2,3))
plot(IC2, main = TRUE, panel.first= grid(), 
     ylim=c(-3,3,-1,3), xlim=c(-2,3),
     with.legend = TRUE)

data <- r(N)(30)
plot(IC2, data, panel.first= grid(),
     ylim = c(-3,3,-1,3), xlim=c(-2,3),
     cex.pts = 3, pch.pts = 1:2, col.pts="green",
     with.lab = TRUE, which.lbs = c(1:4,15:20),
     which.Order = 1:6, return.Order = TRUE)

[Package RobAStBase version 1.2.5 Index]