xyplot                package:lattice                R Documentation

Common Bivariate Trellis Plots

Description:

     These are the most commonly used high level Trellis functions to
     plot pairs of variables. By far the most common is 'xyplot',
     designed mainly for two continuous variates (though factors can be
     supplied as well, in which case they will simply be coerced to
     numeric), which produces Conditional Scatter plots. The others are
     useful when one of the variates is a factor or a shingle.  Most of
     these arguments are also applicable to other high level functions
     in the lattice package, but are only documented here.

Usage:

     xyplot(x, data, ...)
     dotplot(x, data, ...)
     barchart(x, data, ...)
     stripplot(x, data, ...)
     bwplot(x, data, ...)

     ## S3 method for class 'formula':
     xyplot(x,
            data,
            allow.multiple = is.null(groups) || outer,
            outer = !is.null(groups),
            auto.key = FALSE,
            aspect = "fill",
            panel = lattice.getOption("panel.xyplot"),
            prepanel = NULL,
            scales = list(),
            strip = TRUE,
            groups = NULL,
            xlab,
            xlim,
            ylab,
            ylim,
            drop.unused.levels = lattice.getOption("drop.unused.levels"),
            ...,
            lattice.options = NULL,
            default.scales,
            subscripts = !is.null(groups),
            subset = TRUE)

     ## S3 method for class 'formula':
     dotplot(x,
             data,
             panel = lattice.getOption("panel.dotplot"),
             ...)

     ## S3 method for class 'formula':
     barchart(x,
              data,
              panel = lattice.getOption("panel.barchart"),
              box.ratio = 2,
              ...)

     ## S3 method for class 'formula':
     stripplot(x,
               data,
               panel = lattice.getOption("panel.stripplot"),
               ...)

     ## S3 method for class 'formula':
     bwplot(x,
            data,
            allow.multiple = is.null(groups) || outer,
            outer = FALSE,
            auto.key = FALSE,
            aspect = "fill",
            panel = lattice.getOption("panel.bwplot"),
            prepanel = NULL,
            scales = list(),
            strip = TRUE,
            groups = NULL,
            xlab,
            xlim,
            ylab,
            ylim,
            box.ratio = 1,
            horizontal = NULL,
            drop.unused.levels = lattice.getOption("drop.unused.levels"),
            ...,
            lattice.options = NULL,
            default.scales,
            subscripts = !is.null(groups),
            subset = TRUE)

Arguments:

       x: The object on which method dispatch is carried out.

          For the '"formula"' methods, a formula describing the form of
          conditioning plot. The formula is generally of the form 'y ~
          x | g1 * g2 * ...', indicating that plots of 'y' (on the y
          axis) versus 'x' (on the x axis) should be produced
          conditional on the variables 'g1, g2, ...'. However, the
          conditioning variables 'g1,g2,...' may be omitted. The
          formula can also be supplied as 'y ~ x | g1 + g2 + ...'.

          For all of these functions, with the exception of 'xyplot', a
          formula of the form ' ~ x | g1 * g2 * ...' is also allowed.
          In that case, 'y' defaults to 'names(x)' if 'x' is named, and
          a factor with a single level otherwise.

          Other usage of the form 'dotplot(x)' is handled by method
          dispatch as appropriate.  The 'numeric' method is equivalent
          to a call with no left hand side and no conditioning
          variables in the formula.  For 'barchart' and 'dotplot',
          non-trivial methods exist for tables and arrays, documented
          under 'barchart.table'.

          The conditioning variables 'g1, g2, ...' must be either
          factors or shingles.  Shingles are a way of processing
          numeric variables for use in conditioning. See documentation
          of 'shingle' for details. Like factors, they have a
          '"levels"' attribute, which is used in producing the
          conditional plots.

          Numeric conditioning variables are converted to shingles by
          the function 'shingle' (however, using 'equal.count' might be
          more appropriate in many cases) and character vectors are
          coerced to factors.

          The formula can involve expressions, e.g. 'sqrt()', 'log()'.

          A special case is when the left and/or right sides of the
          formula (before the conditioning variables) contain a '+'
          sign, e.g., 'y1+y2 ~ x | a*b'. This formula would be taken to
          mean that the user wants to plot both 'y1~x | a*b' and 'y2~x
          | a*b', but with the 'y1~x' and 'y2~x' superposed in each
          panel (this is slightly more complicated in 'barchart'). The
          two parts would be distinguished by different graphical
          parameters. This is essentially what the 'groups' argument
          would produce, if 'y1' and 'y2' were concatenated to produce
          a longer vector, with the 'groups' argument being an
          indicator of which rows come from which variable.  In fact,
          this is exactly what is done internally using the 'reshape'
          function. This feature cannot be used in conjunction with the
          'groups' argument.  

          To interpret 'y1 + y2' as a sum, one can either set
          'allow.multiple=FALSE' or use 'I(y1+y2)'.

          A variation on this feature is when the 'outer' argument is
          set to 'TRUE' as well as 'allow.multiple'. In that case, the
          plots are not superposed in each panel, but instead separated
          into different panels (as if a new conditioning variable had
          been added).

          The 'x' and 'y' variables should both be numeric in 'xyplot',
          and an attempt is made to coerce them if not. However, if
          either is a factor, the levels of that factor are used as
          axis labels. In the other four functions documented here,
          exactly one of 'x' and 'y' should be numeric, and the other a
          factor or shingle. Which of these will happen is determined
          by the 'horizontal' argument - if 'horizontal=TRUE', then 'y'
          will be coerced to be a factor or shingle, otherwise 'x'. The
          default value of 'horizontal' is 'FALSE' if 'x' is a factor
          or shingle, 'TRUE' otherwise. (The functionality provided by
          'horizontal=FALSE' is not S-compatible.)

          Note that this argument used to be called 'formula' in
          earlier versions (when the high level functions were not
          generic and the formula method was essentially the only
          method).  This is no longer allowed.  It is recommended that
          this argument not be named in any case, but rather be the
          first (unnamed) argument.

    data: For the 'formula' method, a data frame containing values (or
          more precisely, anything that is a valid 'envir' argument in
          'eval', e.g. a list or an environment) for any variables in
          the formula, as well as 'groups' and 'subset' if applicable. 
          If not found in 'data', or if 'data' is unspecified, the
          variables are looked for in the environment of the formula. 
          For other methods (where 'x' is not a formula), 'data' is
          usually ignored, often with a warning. 

allow.multiple, outer: logical flags to control what happens with
          formulas like 'y1 + y2 ~ x'. See the entry for 'x' for
          details. 'allow.multiple' defaults to 'TRUE' whenever it
          makes sense, and 'outer' defaults to 'FALSE' except when
          'groups' is explicitly specified or grouping doesn't make
          sense for the default panel function 

box.ratio: applicable to 'bwplot', 'barchart' and 'stripplot',
          specifies the ratio of the width of the rectangles to the
          inter rectangle space. 

horizontal: logical, applicable to 'bwplot, dotplot, barchart' and
          'stripplot'. Determines which of 'x' and 'y' is to be a
          factor or shingle ('y' if TRUE, 'x' otherwise). Defaults to
          'FALSE' if 'x' is a factor or shingle, 'TRUE' otherwise. This
          argument is used to process the   arguments to these high
          level functions, but more importantly, it is passed as an
          argument to the panel function, which is supposed to use it
          as appropriate.

          A potentially useful component of 'scales' in this case might
          be 'abbreviate = TRUE', in which case long labels which would
          usually overlap will be abbreviated. 'scales' could also
          contain a 'minlength' argument in this case, which would be
          passed to the 'abbreviate' function. 

   panel: Once the subset of rows defined by each unique combination of
          the levels of the grouping variables are obtained (see
          details), the corresponding 'x' and 'y' variables (or other
          variables, as appropriate, in the case of other high level
          functions) are passed on to be plotted in each panel. The
          actual plotting is done by the function specified by the
          'panel' argument.  Each high level function has its own
          default panel function, which could depend on whether the
          'groups' argument was supplied.

          The panel function can be a function object or a character
          string giving the name of a predefined function.

          Much of the power of Trellis Graphics comes from the ability
          to define customized panel functions.  A panel function
          appropriate for the functions described here would usually
          expect arguments named 'x' and 'y', which would be provided
          by the conditioning process.  It can also have other
          arguments. It might be useful to know in this context that
          all arguments passed to a high level Trellis function (such
          as 'xyplot') that are not recognized by it are passed through
          to the panel function. It is thus generally good practice
          when defining panel functions to allow a '...' argument. Such
          extra arguments typically control graphical parameters, but
          other uses are also common. See documentation for individual
          panel functions for specifics.

          Note that unlike in S-PLUS, it is not guaranteed that panel
          functions will be supplied only numeric vectors for the 'x'
          and 'y' arguments; they can be factors as well (but not
          shingles).  Panel functions need to handle this case, which
          in most cases can be done by simply coercing them to numeric.

          Technically speaking, panel functions must be written using
          Grid graphics functions.  However, knowledge of Grid is
          usually not necessary to construct new custom panel
          functions, there are several predefined panel functions which
          can help; for example, 'panel.grid', 'panel.loess', etc. 
          There are also some grid-compatible replacements of commonly
          used base R graphics functions useful for this purpose.  For
          example, 'lines' can be replaced by 'llines' (or
          equivalently, 'panel.lines'). Note that base R graphics
          functions like 'lines' will not work in a lattice panel
          function.

          One case where a bit more is required of the panel function
          is when the 'groups' argument is not null. In that case, the
          panel function should also accept arguments named 'groups'
          and 'subscripts' (see below for details).  A useful panel
          function predefined for use in such cases is
          'panel.superpose', which can be combined with different
          'panel.groups' functions determining what is plotted for each
          group.  See the examples section for an interaction plot
          constructed in this way.  Several other panel functions can
          also handle the 'groups' argument, including the default ones
          for 'barchart', 'dotplot' and 'stripplot'.

          Even when 'groups' is not present, the panel function can
          have 'subscripts' as a formal argument.  In either case, the
          'subscripts' argument passed to the panel function are the
          indices of the 'x' and 'y' data for that panel in the
          original 'data', BEFORE taking into account the effect of the
          'subset' argument.  Note that 'groups' remains unaffected by
          any subsetting operations, so 'groups[subscripts]' gives the
          values of 'groups' that correspond to the data in that panel.

          This interpretation of 'subscripts' does not hold when the
          extended formula interface is in use (i.e., when
          'allow.multiple' is in effect).  A comprehensive description
          would be too complicated (details can be found in the source
          code of the function 'latticeParseFormula'), but in short,
          the extended interface works by creating an artificial
          grouping variable that is longer than the original data
          frame, and consequently, 'subscripts' needs to refer to rows
          beyond those in the original data.  To further complicate
          matters, the artificial grouping variable is created after
          any effect of 'subset', in which case 'subscripts' has
          practically no relationship with corresponding rows in the
          original data frame.

          One can also use functions called 'panel.number' and
          'packet.number', representing panel order and packet order
          respectively, inside the panel function (as well as the strip
          function or while interacting with a lattice display using
          'trellis.focus' etc).  Both provide a simple integer index
          indicating which panel is currently being drawn, but differ
          in how the count is calculated.  The panel number is a simple
          incremental counter that starts with 1 and is incremented
          each time a panel is drawn.  The packet number on the other
          hand indexes the combination of levels of the conditioning
          variables that is represented by that panel.  The two indices
          coincide unless the order of conditioning variables is
          permuted and/or the plotting order of levels within one or
          more conditioning variables is altered (using 'perm.cond' and
          'index.cond' respectively), in which case 'packet.number'
          gives the index corresponding to the 'natural' ordering of
          that combination of levels of the conditioning variables.

          'panel.xyplot' has an argument called 'type' which is worth
          mentioning here because it is quite frequently used (and as
          mentioned above, can be passed to 'xyplot' directly).  In the
          event that a 'groups' variable is used, 'panel.xyplot' calls
          'panel.superpose', arguments of which can also be passed
          directly to 'xyplot'. Panel functions for 'bwplot' and
          friends should have an argument called 'horizontal' to
          account for the cases when 'x' is the factor or shingle. 

  aspect: controls physical aspect ratio of the panels (same for all
          the panels). It can be specified as a ratio (vertical
          size/horizontal size) or as a character string. Legitimate 
          values are '"fill"' (the default) which tries to make the
          panels as big as possible to fill the available space;
          '"xy"', which *tries* to compute the aspect based on the 45
          degree banking rule (see _Visualizing Data_ by William S.
          Cleveland for details); and '"iso"' for isometric scales,
          where the relation between physical distance on the device
          and distance in the data scale are forced to be the same for
          both axes.

          If a 'prepanel' function is specified and it returns
          components 'dx' and 'dy', these are used for banking
          calculations. Otherwise, values from the default prepanel
          function are used. Currently, only the default prepanel
          function for 'xyplot' can be expected to produce sensible
          banking calculations.  See 'banking' for details on the
          implementation of banking . 

  groups: a variable or expression to be evaluated in the data frame
          specified by 'data', expected to act as a grouping variable
          within each panel, typically used to distinguish different
          groups by varying graphical parameters like color and line
          type. Formally, if 'groups' is specified, then 'groups' along
          with 'subscripts' is passed to the panel function, which is
          expected to handle these arguments.  Not all pre-defined
          panel functions know how to, but for high level functions
          where grouping is appropriate, the default panel functions
          are chosen so that they do.

          It is very common to use a key (legend) when a grouping
          variable is specified.  See entries for 'key', 'auto.key' and
          'simpleKey' for how to draw a key. 

auto.key: A logical (indicating whether a key is to be drawn
          automatically when a grouping variable is present in the
          plot), or a list of parameters that would be valid arguments
          to 'simpleKey' (in effect, most valid components of 'key' can
          be specified in this manner).  If 'auto.key' is not 'FALSE',
          'groups' is non-null and there is no 'key' or 'legend'
          argument specified in the call, a key is created with
          'simpleKey' with 'levels(groups)' as the first argument.
          (Note: this may not work in all high level functions, but it
          does work for the ones where grouping makes sense with the
          default panel function)

          'simpleKey' uses the trellis settings to determine the
          graphical parameters in the key, so this will be meaningful
          only if the settings are used in the plot as well.

          One disadvantage to using 'key' (or even 'simpleKey')
          directly is that the graphical parameters used in the key are
          absolutely determined at the time when the '"trellis"' object
          is created. Consequently, if a plot once created is
          re-'print'ed with different settings, the parameter settings
          for the original device will be used. However, with
          'auto.key', the key is actually created at printing time, so
          the key settings will match the device settings. 

prepanel: function that takes the same arguments as the 'panel'
          function and returns a list, possibly containing components
          named 'xlim', 'ylim', 'dx' and 'dy' (and less frequently,
          'xat' and 'yat').

          The 'xlim' and 'ylim' components are similar to the high
          level 'xlim' and 'ylim' arguments (i.e., they are usually a
          numeric vector of length 2 defining a range of values, or a
          character vector representing levels of a factor).  If the
          'xlim' and 'ylim' arguments are not explicitly specified
          (possibly as components in 'scales'), then the actual limits
          of the panels are guaranteed to include the limits returned
          by the prepanel function. This happens globally if the
          'relation' component of 'scales' is '"same"', and on a panel
          by panel basis otherwise. See 'xlim' to see what forms of the
          components 'xlim' and 'ylim' are allowed.

          The 'dx' and 'dy' components are used for banking
          computations in case 'aspect' is specified as '"xy"'.  See
          documentation for the function 'banking' for details
          regarding how this is done.

          The return value of the prepanel function need not have all
          the components named above; in case some are missing, they
          are replaced by the usual component-wise defaults.

          If 'xlim' or 'ylim' is a character vector (which is
          appropriate when the corresponding variable is a factor),
          this implicitly indicates that the scale should include the
          first 'n' integers, where 'n' is the length of 'xlim' or
          'ylim', as the case may be.  The elements of the character
          vector are used as the default labels for these 'n' integers.
          Thus, to make this information consistent between panels, the
          'xlim' or 'ylim' values should represent all the levels of
          the corresponding factor, even if some are not used within
          that particular panel.

          In such cases, an additional component 'xat' or 'yat' may be
          returned by the 'prepanel' function, which should be a subset
          of '1:n', indicating which of the 'n' values (levels) are
          actually represented in the panel.  This is useful when
          calculating the limits with 'relation="free"' or
          'relation="sliced"' in 'scales'.

          The prepanel function is responsible for providing a
          meaningful return value when the 'x', 'y' (etc.) variables
          are zero-length vectors.  When nothing is appropriate, values
          of NA should be returned for the 'xlim' and 'ylim'
          components. 

   strip: logical flag or function.  If 'FALSE', strips are not drawn.
          Otherwise, strips are drawn using the 'strip' function, which
          defaults to 'strip.default'.  See documentation of
          'strip.default' to see the arguments that are available to
          the strip function.  This description also applies to the
          'strip.left' argument (see '...' below), which can be used to
          draw strips on the left of each panel, which can be useful
          for wide short panels, e.g. in time series plots. 

    xlab: character string or expression (or a '"grob"') giving label
          for the x-axis.  Defaults to the expression for 'x' in
          'formula'.  Can be specified as 'NULL' to omit the label
          altogether.  Finer control is possible, as described in the
          entry for 'main', with the additional feature that if the
          'label' component is omitted from the list, it is replaced by
          the default 'xlab'. 

    ylab: character string or expression (or '"grob"') giving label for
          the y-axis.  Defaults to the expression for 'y' in 'formula'.
           Fine control is possible, see entries for 'main' and 'xlab'. 

  scales: list determining how the x- and y-axes (tick marks and
          labels) are drawn.  The list contains parameters in
          'name=value' form, and may also contain two other lists
          called 'x' and 'y' of the same form (described below).
          Components of 'x' and 'y' affect the respective axes only,
          while those in 'scales' affect both.  When parameters are
          specified in both lists, the values in 'x' or 'y' are used. 
          Note that certain high-level functions have defaults that are
          specific to a particular axis (e.g., 'bwplot' has
          'alternating=FALSE' for the y-axis only); these can be
          overridden only by an entry in the corresponding component of
          'scales'.

          The possible components are :


          'relation' character string that determines how axis limits
               are calculated for each panel.  Possible values are
               '"same"' (default), '"free"' and '"sliced"'.  For
               'relation="same"', the same limits, usually large enough
               to encompass all the data, are used for all the panels. 
               For 'relation="free"', limits for each panel is
               determined by just the points in that panel. Behavior
               for 'relation="sliced"' is similar, except that the
               length (max - min) of the scales are constrained to
               remain the same across panels.

               The determination of what axis limits are suitable for
               each panel can be controlled by the 'prepanel' function,
               which can be overridden by 'xlim', 'ylim' or
               'scales$limits'.  If relation is not '"same"', the value
               of 'xlim' etc is normally ignored, except when it is a
               list, in which case it is treated as if its components
               were the limit values obtained from the prepanel
               calculations for each panel.

          'tick.number' Suggested number of ticks (ignored for a
               factor, shingle or character vector, in which case there
               is no natural rule for leaving out some of the labels.
               But see 'xlim').

          'draw' logical, defaults to 'TRUE', whether to draw the axis
               at all.

          'alternating' logical specifying whether axis labels should
               alternate from one side of the group of panels to the
               other.  For finer control, alternating can be a vector
               (replicated to be as long as the number of rows or
               columns per page) consisting of the following numbers

                  *  0: do not draw tick labels

                  *  1: bottom/left

                  *  2: top/right

                  *  3: both.

               'alternating' applies only when 'relation="same"'. The
               default is 'TRUE', or equivalently, 'c(1, 2)'

          'limits' same as xlim and ylim.

          'at' location of tick marks along the axis (in native
               coordinates), or a list as long as the number of panels
               describing tick locations for each panel.

          'labels' Labels (strings or expressions) to go along with
               'at'. Can be a list like 'at' as well.

          'cex' numeric multiplier to control character sizes for axis
               labels. Can be a vector of length 2, to control
               left/bottom and right/top separately.

          'font', 'fontface', 'fontfamily' specifies font for axis
               labels.

          'tck' numeric to control length of tick marks. Can be a
               vector of length 2, to control left/bottom and right/top
               separately.

          'col' color of ticks and labels.

          'rot' Angle by which the axis labels are to be rotated. Can
               be a vector of length 2, to control left/bottom and
               right/top separately.

          'abbreviate' logical, whether to abbreviate the labels using
               'abbreviate'.  Can be useful for long labels (e.g., in
               factors), especially on the x-axis.

          'minlength' argument passed to 'abbreviate' if
               'abbreviate=TRUE'.

          'log' Controls whether the corresponding variable ('x' or
               'y') will be log transformed before being passed to the
               panel function.  Defaults to 'FALSE', in which case the
               data are not transformed.  Other possible values are any
               number that works as a base for taking logarithm, 'TRUE'
               (which is equivalent to 10), and '"e"' (for the natural
               logarithm).  As a side effect, the corresponding axis is
               labeled differently.  Note that this is a transformation
               of the data, not the axes.  Other than the axis
               labeling, using this feature is no different than
               transforming the data in the formula; e.g.,
               'scales=list(x = list(log = 2))' is equivalent to 'y ~
               log2(x)'.  


          'format' the 'format' to use for POSIXct variables. See
               'strptime' for description of valid values.

          'axs' character, '"r"' or '"i"'.  In the latter case, the
               axis limits are calculated as the exact data range,
               instead of being padded on either side. (May not always
               work as expected.)


          Note that much of the function of 'scales' is accomplished by
          'pscales' in 'splom'. 

subscripts: logical specifying whether or not a vector named
          'subscripts' should be passed to the panel function. 
          Defaults to 'FALSE', unless 'groups' is specified, or if the
          panel function accepts an argument named 'subscripts'. (One
          should be careful when defining the panel function
          on-the-fly.) 

  subset: logical or integer indexing vector (can be specified in terms
          of variables in 'data').  Only these rows of 'data' will be
          used for the plot.  If 'subscripts' is 'TRUE', the subscripts
          will provide indices to the rows of data before the
          subsetting is done.  Whether levels of factors in the data
          frame that are unused after the subsetting will be dropped
          depends on the 'drop.unused.levels' argument. 

    xlim: Normally a numeric vector of length 2 (possibly a DateTime
          object) giving minimum and maximum for the x-axis, or, a
          character vector, expected to denote the levels of 'x'.  The
          latter form is interpreted as a range containing c(1,
          length(xlim)), with the character vector determining labels
          at tick positions '1:length(xlim)'

          'xlim' could also be a list, with as many components as the
          number of panels (recycled if necessary), with each component
          as described above.  This is meaningful only when
          'scales$x$relation' is '"free"' or '"sliced"', in which case
          these are treated as if they were the corresponding limit
          components returned by prepanel calculations.

    ylim: similar to 'xlim', applied to the y-axis. 

drop.unused.levels: logical indicating whether the unused levels of
          factors will be dropped, usually relevant with a subsetting
          operation is performed or an 'interaction' is created. 
          Unused levels are usually dropped, but it is sometimes
          appropriate to suppress dropping to preserve a useful layout.
           For finer control, this argument could also be list
          containing components 'cond' and 'data', both logical,
          indicating desired behavior for conditioning variables and
          data variables respectively.  The default is given by
          'lattice.getOption("drop.unused.levels")', which is initially
          set to 'TRUE' for both components.  Note that this argument
          does not control dropping of levels of the 'groups' argument. 

 default.scales : list giving the default values of 'scales' for a
          particular high level function.  This should not be of any
          interest to the normal user, but may be helpful when defining
          other functions that act as a wrapper to one of the high
          level lattice functions. 

lattice.options: a list that could be supplied to 'lattice.options'.
          These options are temporarily in effect for the duration of
          the call, after which the settings revert back to whatever
          they were before.  The settings are also retained along with
          the object and reused during plotting.  This enables the user
          to attach options settings to the trellis object itself
          rather than change the settings globally.  See also the 
          'par.settings' argument described below for a similar
          treatment of graphical settings. 

     ...: further arguments, usually not directly processed by the high
          level functions documented here, but rather passed on to
          other functions. Such arguments can be broadly categorized
          into two types: those that affect all high level Trellis
          functions in a similar manner, and those that are meant for
          the specific panel function used, which may differ across
          high level functions.

          The first group of arguments are processed by a common,
          unexported function called 'trellis.skeleton'.  These
          arguments affect all high level functions, but are only
          documented here, except to override the behaviour described
          here.  All other arguments specified in a high level call,
          specifically those neither described here nor in the help
          page of the relevant high level function, are passed
          unchanged to the panel function used.  By convention, the
          default panel function used for any high level function is
          named as '"panel."' followed by the name of the high level
          function;  for example, the default panel function for
          'bwplot' is 'panel.bwplot'.  In practical terms, this means
          that in addition to the help page of the high level function
          being used, the user should also consult the help page of the
          corresponding panel function for arguments that may be
          specified in the high level call.

          The effect of the first group of common arguments are as
          follows:



          'as.table': logical that controls the order in which panels
               should be plotted: if 'FALSE' (the default), panels are
               drawn left to right, bottom to top (as in a graph); if
               'TRUE', left to right, top to bottom.


          'between': a list with components 'x' and 'y' (both usually 0
               by default), numeric vectors specifying the space
               between the panels (units are character heights). 'x'
               and 'y' are repeated to account for all panels in a page
               and any extra components are ignored. The result is used
               for all pages in a multi page display. (In other words,
               it is not possible to use different 'between' values for
               different pages).


          'key': A list of arguments that define a legend to be drawn
               on the plot. This list is used as an argument to the
               'draw.key' function, which produces a grid object
               eventually plotted by the print method for '"trellis"'
               objects.

               There is also a less flexible but usually sufficient
               shortcut function 'simpleKey' that can generate such a
               list, as well as the argument 'auto.key' that can be
               convenient in the most common situation where legends
               are used, namely when there is a grouping variable. To
               use more than one legend, or to have arbitrary legends
               not constrained by the structure imposed by 'key', use
               the 'legend' argument.

               The position of the key can be controlled in either of
               two possible ways. If a component called 'space' is
               present, the key is positioned outside the plot region,
               in one of the four sides, determined by the value of
               'space', which can be one of '"top"', '"bottom"',
               '"left"' and '"right"'.  Alternatively, the key can be
               positioned inside the plot region by specifying
               components 'x', 'y' and 'corner'. 'x' and 'y' determine
               the location of the corner of the key given by 'corner',
               which is usually one of 'c(0,0)', 'c(1,0)', 'c(1,1)' and
               'c(0,1)', which denote the corners of the unit square.
               Fractional values are also allowed, in which case 'x'
               and 'y' determine the position of an arbitrary point
               inside (or outside for values outside the unit interval)
               the key.

               'x' and 'y' should be numbers between 0 and 1, giving
               coordinates with respect to the "display area".
               Depending on the value of
               'lattice.getOption("legend.bbox")', this can be either
               the full figure region ('"full"'), or just the region
               that bounds the panels and strips ('"panel"').

               The key essentially consists of a number of columns,
               possibly divided into blocks, each containing some rows.
                The contents of the key are determined by (possibly
               repeated) components named '"rectangles"', '"lines"',
               '"points"' or '"text"'.  Each of these must be lists
               with relevant graphical parameters (see later)
               controlling their appearance.  The 'key' list itself can
               contain graphical parameters, these would be used if
               relevant graphical components are omitted from the other
               components.

               The length (number of rows) of each such column (except
               '"text"'s) is taken to be the largest of the lengths of
               the graphical components, including the ones specified
               outside (see the entry for 'rep' below for details on
               this). The '"text"' component has to have a character or
               expression vector as its first component, and the length
               of this vector determines the number of rows.

               The graphical components that can be included in 'key'
               (and also in the components named '"text"', '"lines"',
               '"points"' and '"rectangles"' as appropriate) are:

                  *  'cex=1'

                  *  'col="black"'

                  *  'alpha=1'

                  *  'lty=1'

                  *  'lwd=1'

                  *  'font=1'

                  *  'fontface'

                  *  'fontfamily'

                  *  'pch=8'

                  *  'adj=0'

                  *  'type="l"'

                  *  'size=5'

                  *  'angle=0'

                  *  'density=-1'

               'angle' and 'density' are currently unimplemented.
               'size' determines the width of columns of rectangles and
               lines in character widths. 'type' is relevant for lines;
               '"l"' denotes a line, '"p"' denotes a point, and '"b"'
               and '"o"' both denote both together.

               Other possible components of 'key' are:

               'reverse.rows' logical, defaulting to 'FALSE'.  If
                    'TRUE', all components are reversed _after_ being
                    replicated (the details of which may depend on the
                    value of 'rep').  This is useful in certain
                    situations, e.g. with a grouped 'barchart' with
                    'stack = FALSE' with the categorical variable on
                    the vertical axis, where the bars in the plot will
                    usually be ordered from bottom to top, but the
                    corresponding legend will have the levels from top
                    to bottom (unless, of course, 'reverse.rows =
                    TRUE').  Note that in this case, unless all columns
                    have the same number or rows, they will no longer
                    be aligned.

               'between' numeric vector giving the amount of space
                    (character widths) surrounding each column (split
                    equally on both sides)

               'title' string or expression giving a title for the key

               'rep' logical, defaults to 'TRUE'.  By default, it's
                    assumed that all columns in the key (except the
                    '"text"'s) will have the same number of rows, and
                    all components are replicated to be as long as the
                    longest. This can be suppressed by specifying
                    'rep=FALSE', in which case the length of each
                    column will be determined by components of that
                    column alone.

               'cex.title' cex for the title

               'lines.title' how many lines the title should occupy (in
                    multiples of itself).  Defaults to 2.

               'padding.text' how much space (padding) should be used
                    above and below each row containing text, in
                    multiples of the default, which is currently '0.2 *
                    "lines"'.  This padding is in addition to the
                    normal height of any row that contains text, which
                    is the minimum amount necessary to contain all the
                    text entries.

               'background' background color, defaults to default
                    background

               'alpha.background' An alpha transparency value between 0
                    and 1

               'border' either a color for the border, or a logical. 
                    In the latter case, the border color is black if
                    'border' is 'TRUE', and no border is drawn if it is
                    'FALSE' (the default)

               'transparent=FALSE' logical, whether key area should
                    have a transparent background

               'columns' the number of columns column-blocks the key is
                    to be divided into, which are drawn side by side.

               'between.columns' Space between column blocks, in
                    addition to 'between'.

               'divide' Number of point symbols to divide each line
                    when 'type' is '"b"' or '"o"' in 'lines'.


          'legend': the legend argument can be useful if one wants to
               place more than one key. It also allows one to use
               arbitrary '"grob"'s (grid objects) as legends.

               If used, 'legend' must be a list, with an arbitrary
               number of components. Each component must be named one
               of '"left"', '"right"', '"top"', '"bottom"' or
               '"inside"'. The name '"inside"' can be repeated, but not
               the others.  This name will be used to determine the
               location for that component, and is similar to the
               'space' component of 'key'.  If 'key' (or 'colorkey' for
               'levelplot' and 'wireframe') is specified, their 'space'
               component must not conflict with the name of any
               component of 'legend'.

               Each component of 'legend' must have a component called
               'fun'. This can be a '"grob"', or a function or the name
               of a function that produces a '"grob"' when called. If
               this function expects any arguments, they must be
               supplied as a list in another component called 'args'.
               For components named '"inside"', there can be additional
               components called 'x', 'y' and 'corner', which work in
               the same way as it does for 'key'.


          'page': a function of one argument (page number) to be called
               after drawing each page. The function must be
               'grid-compliant', and is called with the whole display
               area as the default viewport.

          'main': typically a character string or expression describing
               the main title to be placed on top of each page.
               Defaults to 'NULL'.  'main' (as well as 'xlab', 'ylab'
               and 'sub') is usually a character string or an
               expression that gets used as the label, but can also be
               a list that controls further details.  Expressions are
               treated as specification of LaTeX-like markup as
               described in 'plotmath'.  The label can be a vector, in
               which case the components will be spaced out
               horizontally (or vertically for 'ylab').  This feature
               can be used to provide column or row labels rather than
               a single axis label.

               When 'main' (etc.) is a list, the actual label should be
               specified as the 'label' component (which may be unnamed
               if it is the first component).  The label can be
               missing, in which case the default will be used ('xlab'
               and 'ylab' usually have defaults, but 'main' and 'sub'
               do not). Further named arguments are passed on to
               'textGrob'; this can include arguments controlling
               positioning like 'just' and 'rot' as well as graphical
               parameters such as 'col' and 'font' (see 'gpar' for a
               full list).

               'main', 'xlab', 'ylab' and 'sub' can also be an
               arbitrary '"grob"' (grid graphical object).

          'sub': character string or expression (or a list or '"grob"')
               for a subtitle to be placed at the bottom of each page. 
               See entry for 'main' for finer control options.

          'par.strip.text': list of  parameters to control the
               appearance of strip text.  Notable components are 'col',
               'cex', 'font' and 'lines'.  The first three control
               graphical parameters while the last is a means of
               altering the height of the strips.  This can be useful,
               for example, if the strip labels (derived from factor
               levels, say) are double height (i.e., contains '"\n"'-s)
               or if the default height seems too small or too large. 
               The 'lineheight' component can control the space between
               multiple lines.  Also, the labels can be abbreviated
               when shown by specifying 'abbreviate = TRUE', in which
               case the components 'minlength' and 'dot' (passed along
               to the 'abbreviate' function) can be specified to
               control the details of how this is done.

          'layout': In general, a Trellis conditioning plot consists of
               several panels arranged in a rectangular array, possibly
               spanning multiple pages. 'layout' determines this
               arrangement.

               'layout' is a numeric vector giving the number of
               columns, rows and pages in a multi panel display.  By
               default, the number of columns is the number of levels
               of the first conditioning variable and the number of
               rows is the number of levels of the second conditioning
               variable.  If there is only one conditioning variable,
               the default layout vector is 'c(0,n)', where 'n' is the
               number of levels of the given vector.  Any time the
               first value in the layout vector is 0, the second value
               is used as the desired number of panels per page and the
               actual layout is computed from this, taking into account
               the aspect ratio of the panels and the device dimensions
               (via 'par("din")').  The number of pages is by default
               set to as many as is required to plot all the panels. 
               In general, giving a high value of 'layout[3]' is not
               wasteful because blank pages are never created.

          'skip': logical vector (default 'FALSE'), replicated to be as
               long as the number of panels (spanning all pages).  For
               elements that are 'TRUE', the corresponding panel
               position is skipped; i.e., nothing is plotted in that
               position.  The panel that was supposed to be drawn there
               is now drawn in the next available panel position, and
               the positions of all the subsequent panels are bumped up
               accordingly.  This is often useful for arranging plots
               in an informative manner.


          'strip.left': 'strip.left' can be used to draw strips on the
               left of each panel, which can be useful for wide short
               panels, as in time series (or similar) plots.  It is a
               function similar to 'strip'.


          'xlab.default', 'ylab.default': fallback default for 'xlab'
               and 'ylab' when they are not specified.  If 'NULL', the
               defaults are parsed from the Trellis formula. This is
               rarely useful for the end-user, but can be helpful when
               developing new Trellis functions.

          'xscale.components, yscale.components': functions that
               determine axis annotation for the x and y axes
               respectively.  See documentation for
               'xscale.components.default', the default values of these
               arguments, to learn more. 

          'axis': function that draws axis annotation.  See
               documentation for 'axis.default', the default value of
               this argument, to learn more. 

          'perm.cond': numeric vector, a permutation of '1:n', where
               'n' is the number of conditioning variables.  By
               default, the order in which panels are drawn depends on
               the order of the conditioning variables specified in the
               'formula'.  'perm.cond' can modify this order.  If the
               trellis display is thought of as an 'n'-dimensional
               array, then during printing, its dimensions are permuted
               using 'perm.cond' as the 'perm' argument to 'aperm'.

          'index.cond': While 'perm.cond' permutes the dimensions of
               the multidimensional array of panels, 'index.cond' can
               be used to subset (or reorder) margins of that array. 
               'index.cond' can be a list or a function, with behavior
               in each case described below. 

               The panel display order within each conditioning
               variable depends on the order of their levels. 
               'index.cond' can be used to choose a 'subset' (in the R
               sense) of these levels, which is then used as the
               display order for that variable.  If 'index.cond' is a
               list, it has to be as long as the number of conditioning
               variables, and the 'i'-th component has to be a valid
               indexing vector for the integer vector '1:nlevels(g_i)'
               (which can, among other things, repeat some of the
               levels or drop some altogether).  The result of this
               indexing determines the order of panels within that
               conditioning variable. To keep the order of a particular
               variable unchanged, the corresponding component must be
               set to 'TRUE'.

               Note that the components of 'index.cond' are in the
               order of the conditioning variables in the original
               call, and is not affected by 'perm.cond'.

               Another possibility is to specify 'index.cond' as a
               function. In this case, this function is called once for
               each panel, potentially with all arguments that are
               passed to the panel function for that panel. (More
               specifically, if this function has a '...' argument,
               then all panel arguments are passed, otherwise, only
               named arguments that match are passed.) For a single
               conditioning variable, the levels of that variable are
               then sorted so that these values are in ascending order.
               For multiple conditioning variables, the order for each
               variable is determined by first taking the average over
               all other conditioning variables.

               Although they can be supplied in high level function
               calls directly, it is more typical to use 'perm.cond'
               and 'index.cond' to update an existing '"trellis"'
               object, thus allowing it to be displayed in a different
               arrangement without re-calculating the data subsets that
               go into each panel. In the 'update' method, both can be
               set to 'NULL', which reverts these back to their
               defaults.

          'par.settings': a list that could be supplied to
               'trellis.par.set'. This enables the user to attach some
               display settings to the trellis object itself rather
               than change the settings globally.  When the object is
               plotted, these settings are temporarily in effect for
               the duration of the plot, after which the settings
               revert back to whatever they were before.

          'plot.args': a list of possible arguments to 'plot.trellis',
               which will be used by the 'plot' or 'print' methods when
               drawing the object, unless overridden explicitly.  This
               enables the user to attach such arguments to the trellis
               object itself.  Partial matching is not performed.


Details:

     All the functions documented here are generic, with the 'formula'
     method usually doing the actual work.  The structure of the plot
     that is produced is mostly controlled by the formula.  For each
     unique combination of the levels of the conditioning variables
     'g1, g2, ...', a separate panel is produced using the points
     '(x,y)' for the subset of the data (also called packet) defined by
     that combination.  The display can be though of as a 3-dimensional
     array of panels, consisting of one 2-dimensional matrix per page. 
     The dimensions of this array are determined by the 'layout'
     argument. If there are no conditioning variables, the plot
     produced consists of a single panel.

     The coordinate system used by lattice by default is like a graph,
     with the origin at the bottom left, with axes increasing to left
     and up. In particular, panels are by default drawn starting from
     the bottom left corner, going right and then up; unless 'as.table
     = TRUE', in which case panels are drawn from the top left corner,
     going right and then down.  One might wish to set a global
     preference for a table-like arrangement by changing the default to
     'as.table=TRUE'; this can be done by setting
     'lattice.options(default.args = list(as.table = TRUE))'.  In fact,
     default values can be set in this manner for the following
     arguments: 'as.table', 'aspect', 'between', 'page', 'main', 'sub',
     'par.strip.text', 'layout', 'skip' and 'strip'.  Note that these
     global defaults are sometimes overridden by individual functions.

     The order of the panels depends on the order in which the
     conditioning variables are specified, with 'g1' varying fastest.
     Within a conditioning variable, the order depends on the order of
     the levels (which for factors is usually in alphabetical order). 
     Both of these orders can be modified using the 'index.cond' and
     'perm.cond' arguments, possibly using the 'update' (and other
     related) method(s).

Value:

     An object of class '"trellis"'. The 'update' method can be used to
     update components of the object and the 'print' method (usually
     called by default) will plot it on an appropriate plotting device.

Note:

     Most of the arguments documented here are also applicable for the
     other high level functions in the lattice package. These are not
     described in any detail elsewhere unless relevant, and this should
     be considered the canonical documentation for such arguments.

     Any arguments passed to these functions and not recognized by them
     will be passed to the panel function. Most predefined panel
     functions have arguments that customize its output. These
     arguments are described only in the help pages for these panel
     functions, but can usually be supplied as arguments to the high
     level plot.

Author(s):

     Deepayan Sarkar Deepayan.Sarkar@R-project.org

References:

     Sarkar, Deepayan (2008) "Lattice: Multivariate Data Visualization
     with R", Springer. <URL: http://lmdvr.r-forge.r-project.org/>

See Also:

     'Lattice' for an overview of the package, as well as 
     'barchart.table', 'Lattice', 'print.trellis', 'shingle',
     'banking', 'reshape', 'panel.xyplot', 'panel.bwplot',
     'panel.barchart', 'panel.dotplot', 'panel.stripplot',
     'panel.superpose', 'panel.loess', 'panel.linejoin',
     'strip.default', 'simpleKey' 'trellis.par.set'

Examples:

     ## Not run: 
     ## wait for user input before each new page (like 'par(ask = TRUE)')
     old.prompt <- grid::grid.prompt(TRUE)
     ## End(Not run)

     require(stats)

     ## Tonga Trench Earthquakes

     Depth <- equal.count(quakes$depth, number=8, overlap=.1)
     xyplot(lat ~ long | Depth, data = quakes)
     update(trellis.last.object(),
            strip = strip.custom(strip.names = TRUE, strip.levels = TRUE),
            par.strip.text = list(cex = 0.75),
            aspect = "iso")

     ## Examples with data from `Visualizing Data' (Cleveland)
     ## (obtained from Bill Cleveland's Homepage :
     ## http://cm.bell-labs.com/cm/ms/departments/sia/wsc/, also
     ## available at statlib)

     EE <- equal.count(ethanol$E, number=9, overlap=1/4)
     ## Constructing panel functions on the fly; prepanel
     xyplot(NOx ~ C | EE, data = ethanol,
            prepanel = function(x, y) prepanel.loess(x, y, span = 1),
            xlab = "Compression Ratio", ylab = "NOx (micrograms/J)",
            panel = function(x, y) {
                panel.grid(h=-1, v= 2)
                panel.xyplot(x, y)
                panel.loess(x,y, span=1)
            },
            aspect = "xy")


     ## with and without banking

     plot <- xyplot(sunspot.year ~ 1700:1988, xlab = "", type = "l",
                    scales = list(x = list(alternating = 2)),
                    main = "Yearly Sunspots")
     print(plot, position = c(0, .3, 1, .9), more = TRUE)
     print(update(plot, aspect = "xy", main = "", xlab = "Year"),
           position = c(0, 0, 1, .3))



     ## Multiple variables in formula for grouped displays

     xyplot(Sepal.Length + Sepal.Width ~ Petal.Length + Petal.Width | Species, 
            data = iris, scales = "free", layout = c(2, 2),
            auto.key = list(x = .6, y = .7, corner = c(0, 0)))

     ## user defined panel functions

     states <- data.frame(state.x77,
                          state.name = dimnames(state.x77)[[1]], 
                          state.region = state.region) 
     xyplot(Murder ~ Population | state.region, data = states, 
            groups = state.name, 
            panel = function(x, y, subscripts, groups)  
            ltext(x = x, y = y, label = groups[subscripts], cex=1,
                  fontfamily = "HersheySans"))

     barchart(yield ~ variety | site, data = barley,
              groups = year, layout = c(1,6),
              ylab = "Barley Yield (bushels/acre)",
              scales = list(x = list(abbreviate = TRUE,
                            minlength = 5)))
     barchart(yield ~ variety | site, data = barley,
              groups = year, layout = c(1,6), stack = TRUE, 
              auto.key = list(points = FALSE, rectangles = TRUE, space = "right"),
              ylab = "Barley Yield (bushels/acre)",
              scales = list(x = list(rot = 45)))

     bwplot(voice.part ~ height, data=singer, xlab="Height (inches)")
     dotplot(variety ~ yield | year * site, data=barley)

     dotplot(variety ~ yield | site, data = barley, groups = year,
             key = simpleKey(levels(barley$year), space = "right"),
             xlab = "Barley Yield (bushels/acre) ",
             aspect=0.5, layout = c(1,6), ylab=NULL)

     stripplot(voice.part ~ jitter(height), data = singer, aspect = 1,
               jitter = TRUE, xlab = "Height (inches)")
     ## Interaction Plot

     xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos,
            type = "a",
            auto.key =
            list(space = "right", points = FALSE, lines = TRUE))

     ## longer version with no x-ticks

     ## Not run: 
     bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos,
            panel = "panel.superpose",
            panel.groups = "panel.linejoin",
            xlab = "treatment",
            key = list(lines = Rows(trellis.par.get("superpose.line"),
                       c(1:7, 1)), 
                       text = list(lab = as.character(unique(OrchardSprays$rowpos))),
                       columns = 4, title = "Row position"))
     ## End(Not run)

     ## Not run: 
     grid::grid.prompt(old.prompt)
     ## End(Not run)

