R/miscellaneous.R

Defines functions lplot.xy lpoints.default llines.default ltext.default ltext larrows.default larrows lrect.default lrect lsegments.default lsegments lpolypath.default lpolypath lpolygon.default lpolygon primName panel.text panel.segments panel.rect panel.polypath panel.polygon panel.points panel.lines panel.arrows Rows do.breaks updateList scale_limits as.factorOrShingle is.characterOrExpression oneway lpretty chooseFace logLimits hasGroupNumber checkArgsAndCall getFunctionOrName

Documented in as.factorOrShingle do.breaks larrows larrows.default llines.default lplot.xy lpoints.default lpolygon lpolygon.default lpolypath lpolypath.default lrect lrect.default lsegments lsegments.default ltext ltext.default oneway panel.arrows panel.lines panel.points panel.polygon panel.polypath panel.rect panel.segments panel.text Rows

### Copyright (C) 2001-2009 Deepayan Sarkar <Deepayan.Sarkar@R-project.org> 
###
### This file is part of the lattice package for R.
### It is made available under the terms of the GNU General Public
### License, version 2, or at your option, any later version,
### incorporated herein by reference.
###
### This program is distributed in the hope that it will be
### useful, but WITHOUT ANY WARRANTY; without even the implied
### warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
### PURPOSE.  See the GNU General Public License for more
### details.
###
### You should have received a copy of the GNU General Public
### License along with this program; if not, write to the Free
### Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
### MA 02110-1301, USA


## For historical reasons (i.e., S-compatibility) there are several
## places in lattice where an argument that is supposed to be a
## function may be specified as a character string.  It is not
## entirely clear how namespace ambiguity is resolved, but it appears
## that bindings in the lattice namespace are preferred over the
## global environment.


getFunctionOrName <- function(FUN)
     ## Try lattice namespace first? Does that happen automatically?
{
    if (is.function(FUN)) FUN
    else if (is.character(FUN)) get(FUN)
    else eval(FUN)
}


checkArgsAndCall <- function(FUN, args) ## unnamed arguments not allowed
{
    if (!is.null(FUN)) {
        if (!("..." %in% names(formals(FUN))))
            args <- args[intersect(names(args), names(formals(FUN)))]
        do.call(FUN, args, quote = TRUE) ## FIXME: Is this risky?
    }
}


## Modified from methods::hasArg.
hasGroupNumber <- function()
{
    aname <- "group.number"
    fnames <- names(formals(sys.function(sys.parent())))
    if (is.na(match(aname, fnames))) {
        if (is.na(match("...", fnames)))
            FALSE
        else {
            dotsCall <- eval(quote(substitute(list(...))), sys.parent())
            !is.na(match(aname, names(dotsCall)))
        }
    }
    else FALSE
}



logLimits <- function(lim, base)
{
    if (is.list(lim))
        lapply(lim, log, base)
    else log(lim, base)
}


chooseFace <- function(fontface = NULL, font = 1)
{
    if (is.null(fontface)) font else fontface
}


lpretty <- function(x, ...)
{
    eps <- 1e-10
    at <- pretty(x[is.finite(x)], ...)
    ifelse(abs(at-round(at, 3))<eps, round(at, 3), at)
}


oneway <-
    function(formula, data, location = mean,
             spread = function(x) sqrt(var(x)))
{
    if(missing(data)) data <- sys.frame(sys.parent())
    form <- latticeParseFormula(formula, data)
    y <- form$left
    x <- form$right
    if (!is.shingle(x)) x <- as.factor(x)
    is.f.x <- is.factor(x)
    num.l.x <- nlevels(x) 
    foo <- list()
    if (is.f.x) {
        foo$location <-
            if (is.function(location)) as.vector(tapply(X=y, INDEX=list(x), FUN = location))
            else rep(location, num.l.x)
        foo$spread <- 
            if (is.function(spread)) as.vector(tapply(X=y, INDEX=list(x), FUN = spread))
            else rep(spread, num.l.x)
        foo$fitted.values <- numeric(length(y))
        sc <- numeric(length(y))
        for (i in seq_along(y)){
            foo$fitted.values[i] <- foo$location[as.numeric(x)[i]]
            sc[i] <- foo$spread[as.numeric(x)[i]]
        }
        foo$residuals <- y - foo$fitted.values
        foo$scaled.residuals <- foo$residuals/sc
    }
    else stop("x must be (coercible to be) a factor")
    foo
}



is.characterOrExpression <- function(x)
    is.character(x) || is.expression(x) || is.call(x) || is.symbol(x)




## This converts character to factor, numeric to shingle, and
## in addition, takes subsets
as.factorOrShingle <- function(x, subset = TRUE, drop = FALSE)
{
    x <-
        if (is.numeric(x))
            as.shingle(x)
        else ##if (is.character(x)) or logical or ??
            as.factor(x)
    x[subset, drop = drop]
}



## this is a generalization of range(x), used as the xlim/ylim
## components of prepanel functions.  It should deals with factors,
## numerics, and date-time classes.
scale_limits <- function(x)
{
    if (is.factor(x)) levels(x)
    else if (is.numeric(x)) range(x, finite = TRUE)
    else range(x, na.rm = TRUE)
}




## update elements of a list recursively. Used in updating trellis or
## lattice settings using trellis.par.set and lattice.options
## respectively

updateList <- function(x, val)
{
    if (is.null(x)) x <- list()
    modifyList(x, val)
}


##     function(x, val)
## {
##     if (is.null(x)) x <- list()
##     if (!is.list(x)) stop("x must be NULL or a list")
##     if (!is.list(val)) stop("val must be a list")
##     xnames <- names(x)
##     for (v in names(val))
##     {
##         existing <- v %in% xnames
##         if (existing && is.list(x[[v]]) && is.list(val[[v]]))
##             x[[v]] <- updateList(x[[v]], val[[v]])
##         else 
##             x[[v]] <- val[[v]]
##     }
##     x
## }


## Next 3 are convenience functions following those available in Trellis

do.breaks  <- function(endpoints, nint)
{
    if (length(endpoints)!=2) stop("error")
    endpoints[1] + diff(endpoints) * 0:nint / nint
}


Rows <- function(x, which)
{
    for (i in seq_along(x)) x[[i]] <-
        rep(x[[i]], length.out = max(which, length(which)))[which]
    x
}





## panel functions corresponding to standard low-level graphics functions

panel.arrows <- function(...) larrows(...)
panel.lines <- function(...) llines(...)
panel.points <- function(...) lpoints(...)
panel.polygon <- function(...) lpolygon(...)
panel.polypath <- function(...) lpolypath(...)
panel.rect <- function(...) lrect(...)
panel.segments <- function(...) lsegments(...)
panel.text <- function(...) ltext(...)




primName <- function(name, identifier = NULL, name.type = "panel", group = 0) {
    trellis.grobname(name = ifelse(is.null(identifier), name,
                       paste(identifier, name, sep=".")),
                     type = name.type,
                     group = group)
}



## The rest are grid-ified versions of standard base 'incremental
## graphics' functions.  Maybe it's better to push wrappers like
## panel.points, panel.lines, etc.


lpolygon <- function(x, ...) UseMethod("lpolygon")

lpolygon.default <-
    function(x, y = NULL,
             ## density = NULL,
             ## angle = 45,
             border = "black",
             col = "transparent",
             ## lty = NULL,
             fill = NULL, # capture so that doesn't overload 'fill=col' in gpar()

             font, fontface, ## gpar() doesn't like these
             ...,
             rule = c("none", "winding", "evenodd"),
             identifier = NULL,
             name.type = "panel") 
{
    if (sum(!is.na(x)) < 1) return()
    rule <- match.arg(rule)
    border <- 
        if (all(is.na(border))) "transparent"
        else if (is.logical(border))
        {
            if (border) "black" else "transparent"
        }
        else border
    xy <- xy.coords(x, y, recycle = TRUE)
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    n <- length(xy$x)
    breaks <- which(is.na(xy$x) | is.na(xy$y))
    nb <- length(breaks)
    id.lengths <- diff(c(0, breaks, n))
    if (rule == "none" || nb == 0)
        grid.polygon(x = xy$x,
                     y = xy$y,
                     id.lengths = id.lengths,
                     default.units = "native",
                     name = primName("polygon", identifier, name.type, group),
                     gp = gpar(fill = col, col = border, ...))
    else {
        ## grid.polygon() can handle NAs but grid.path() cannot. So we
        ## use a strategy copied from polypath() in lpolypath(). This
        ## should work equally well with grid.polygon(), so eventually
        ## we should change that too.

        ## if (nb == 0) {
        ##      any difference between grid.polygon() and grid.path() ?
        ## }
        lengths <- c(breaks[1] - 1, diff(breaks) - 1, n - breaks[nb])
        grid.path(x = xy$x[-breaks],
                  y = xy$y[-breaks],
                  id.lengths = lengths,
                  rule = rule,
                  default.units = "native",
                  name = primName("path", identifier, name.type, group),
                  gp = gpar(fill = col, col = border, ...))
    }
}


lpolypath <- function(x, ...) UseMethod("lpolypath")

lpolypath.default <-
    function(x, y = NULL,
             border = "black",
             col = "transparent",
             ## lty = NULL,
             fill = NULL, # capture so that doesn't overload 'fill=col' in gpar()

             font, fontface, ## gpar() doesn't like these
             ...,
             rule = c("winding", "evenodd"),
             identifier = NULL,
             name.type = "panel") 
{
    if (sum(!is.na(x)) < 1) return()
    rule <- match.arg(rule)
    border <- 
        if (all(is.na(border))) "transparent"
        else if (is.logical(border))
        {
            if (border) "black" else "transparent"
        }
        else border
    xy <- xy.coords(x, y, recycle = TRUE)
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    n <- length(xy$x)
    breaks <- which(is.na(xy$x) | is.na(xy$y))
    nb <- length(breaks)
    lengths <- c(breaks[1] - 1, diff(breaks) - 1, n - breaks[nb])
    grid.path(x = xy$x[-breaks],
              y = xy$y[-breaks],
              id.lengths = lengths,
              rule = rule,
              default.units = "native",
              name = primName("path", identifier, name.type, group),
              gp = gpar(fill = col, col = border, ...))
}



lsegments <- function(...) UseMethod("lsegments")

lsegments.default <-
    function(x0 = NULL, y0 = NULL, x1, y1,
             x2 = NULL, y2 = NULL,
             col = add.line$col,
             alpha = add.line$alpha,
             lty = add.line$lty,
             lwd = add.line$lwd,

             font, fontface, ## gpar() doesn't like these

             ...,
             identifier = NULL,
             name.type = "panel")
{
    if (missing(x0)) x0 <- x2
    if (missing(y0)) y0 <- y2
    add.line <- trellis.par.get("add.line")
    ml <- max(length(x0), length(x1), length(y0), length(y1))
    x0 <- rep(x0, length.out = ml)
    x1 <- rep(x1, length.out = ml)
    y0 <- rep(y0, length.out = ml)
    y1 <- rep(y1, length.out = ml)
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    grid.segments(x0 = x0, x1 = x1,
                  y0 = y0, y1 = y1,
                  name = primName("segments", identifier, name.type, group),
                  gp =
                  gpar(lty=lty, col = col, lwd = lwd,
                       alpha = alpha, ...),
                  default.units = "native")
}



lrect <- function(...) UseMethod("lrect")

lrect.default <-
    function(xleft, ybottom, xright, ytop,
             x = (xleft + xright) / 2,
             y = (ybottom + ytop) / 2,
             width = xright - xleft,
             height = ytop - ybottom,
             col = "transparent",
             border = "black",
             lty = 1, lwd = 1, alpha = 1,
             just = "center",
             hjust = NULL, vjust = NULL,

             font, fontface, ## gpar() doesn't like these

             ...,
             identifier = NULL,
             name.type = "panel")
{
    border <- 
        if (all(is.na(border)))
            "transparent"
        else if (is.logical(border))
        {
            if (border) "black"
            else "transparent"
        }
        else border
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    grid.rect(x = x, y = y,
              width = width, height = height,
              default.units = "native",
              just = just, hjust = hjust, vjust = vjust,
              name = primName("rect", identifier, name.type, group),
              gp =
              gpar(fill = col, col = border,
                   lty = lty, lwd = lwd,
                   alpha = alpha, ...))
}



larrows <- function(...) UseMethod("larrows")

larrows.default <-
    function(x0 = NULL, y0 = NULL, x1, y1, x2 = NULL, y2 = NULL,
             angle = 30, code = 2, length = 0.25, unit = "inches",
             ends = switch(code, "first", "last", "both"),
             type = "open",
             col = add.line$col,
             alpha = add.line$alpha,
             lty = add.line$lty,
             lwd = add.line$lwd,
             fill = NULL,

             font, fontface, ## gpar() doesn't like these

             ...,
             identifier = NULL,
             name.type = "panel")
{
    if (missing(x0)) x0 <- x2
    if (missing(y0)) y0 <- y2
    add.line <- trellis.par.get("add.line")
    ml <- max(length(x0), length(x1), length(y0), length(y1))
    x0 <- rep(x0, length.out = ml)
    x1 <- rep(x1, length.out = ml)
    y0 <- rep(y0, length.out = ml)
    y1 <- rep(y1, length.out = ml)
    gp <- gpar(col = col, lty = lty, lwd = lwd, alpha = alpha, fill = fill, ...)
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    grid.segments(x0 = x0, x1 = x1,
                  y0 = y0, y1 = y1,
                  name = primName("arrows", identifier, name.type, group),
                  gp = gp,
                  arrow = if (is.null(ends)) NULL else 
                  arrow(angle = angle,
                        length = unit(length, unit),
                        ends = ends,
                        type = type),
                  default.units = "native")
}



ltext <- function(x, ...) UseMethod("ltext")

ltext.default <-
    function(x, y = NULL, labels = seq_along(x),
             col = add.text$col,
             alpha = add.text$alpha,
             cex = add.text$cex,
             srt = 0,
             lineheight = add.text$lineheight,
             font = add.text$font,
             fontfamily = add.text$fontfamily,
             fontface = add.text$fontface,
             adj = c(.5, .5),
             pos = NULL,
             offset = 0.5,
             ...,
             identifier = NULL,
             name.type = "panel")
{
    add.text <- trellis.par.get("add.text")
    xy <- xy.coords(x, y, recycle = TRUE)
    n <- length(xy$x)
    if (n == 0) return()
    ux <- unit(xy$x, "native")
    uy <- unit(xy$y, "native")
    if (length(adj) == 1) adj <- c(adj, .5)
    hjust <- adj[1]
    vjust <- adj[2]
    if (!is.null(pos))
    {
        if (length(pos) == 1) # 'pos' scalar
        {
            hjust <- vjust <- 0.5
            if (pos == 1) {
                uy <- uy - unit(offset, "char")
                vjust <- 1
            }
            else if (pos == 2) {
                ux <- ux - unit(offset, "char")
                hjust <- 1
            }
            else if (pos == 3) {
                uy <- uy + unit(offset, "char")
                vjust <- 0
            }
            else if (pos == 4) {
                ux <- ux + unit(offset, "char")
                hjust <- 0
            }
            else warning("Invalid value of 'pos' ignored.")
        }
        else # 'pos' vector
        {
            ## Note, replacements like x[i] <- something don't work
            ## for "unit" objects, so we have to do full updates.
            pos <- rep(pos, length.out = n)
            hjust <- vjust <- rep(0.5, n)
            if (any(i <- (pos == 1)))
            {
                ## uy[i] <- uy[i] - unit(offset, "char") # no good
                uy <- uy - unit(ifelse(i, offset, 0), "char")
                vjust[i] <- 1
            }
            if (any(i <- (pos == 2)))
            {
                ux <- ux - unit(ifelse(i, offset, 0), "char")
                hjust[i] <- 1
            }
            if (any(i <- (pos == 3)))
            {
                uy <- uy + unit(ifelse(i, offset, 0), "char")
                vjust[i] <- 0
            }
            if (any(i <- (pos == 4)))
            {
                ux <- ux + unit(ifelse(i, offset, 0), "char")
                hjust[i] <- 0
            }
        }
    }
    ## replace non-finite srt by 0
    srt[!is.finite(srt)] <- 0
    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0
    grid.text(label = labels, x = ux, y = uy,
              name = primName("text", identifier, name.type, group),
              gp =
              gpar(col = col, alpha = alpha,
                   lineheight = lineheight,
                   fontfamily = fontfamily,
                   fontface = chooseFace(fontface, font),
                   cex = cex, ...),
              hjust = hjust, vjust = vjust,
              rot = srt)
}



llines <- function (x, ...) UseMethod("llines")


llines.default <-
    function(x, y = NULL, type = "l",
             col = plot.line$col,
             alpha = plot.line$alpha,
             lty = plot.line$lty,
             lwd = plot.line$lwd, ...,
             identifier = NULL,
             name.type = "panel")
{
    plot.line <- trellis.par.get("plot.line")
    lplot.xy(xy.coords(x, y, recycle = TRUE), type = type,
             col = col, lty = lty, lwd = lwd, alpha = alpha, ...,
             identifier = identifier, name.type = name.type)
}


lpoints <- function (x, ...) UseMethod("lpoints")

lpoints.default <-
    function(x, y = NULL, type = "p",
             col = plot.symbol$col,
             pch = plot.symbol$pch,
             alpha = plot.symbol$alpha,
             fill = plot.symbol$fill,
             font = plot.symbol$font,
             fontfamily = plot.symbol$fontfamily,
             fontface = plot.symbol$fontface,
             cex = plot.symbol$cex, ...,
             identifier = NULL,
             name.type = "panel")
{
    plot.symbol <- trellis.par.get("plot.symbol")
    lplot.xy(xy.coords(x, y, recycle = TRUE),
             type = type,
             col = col,
             pch = pch,
             alpha = alpha,
             fill = fill,
             font = font,
             fontfamily = fontfamily,
             fontface = fontface,
             cex = cex,
             ...,
             identifier = identifier,
             name.type = name.type)
}






lplot.xy <-
    function(xy,
             type = c("p", "l", "o", "b", "c", "s", "S", "h", "H"),
             pch = 1, lty = 1, col = 1, cex = 1, lwd = 1,
             font = 1, fontfamily = NULL, fontface = NULL,
             col.line = col, col.symbol = col, alpha = 1, fill = NULL,
             origin = 0,
             ...,
             identifier = NULL,
             name.type = "panel")
{
    x <- xy$x
    y <- xy$y
    fontsize.points <- trellis.par.get("fontsize")$points
    if (length(x) == 0) return()

    ## the main difference between this and panel.xyplot is that the
    ## latter allows vector 'type', this doesn't

    if (hasGroupNumber())
        group <- list(...)$group.number
    else
        group <- 0

    type <- match.arg(type)
    switch(type,
           p = {
               grid.points(x = x, y = y, 
                           name = primName("points", identifier, name.type, group),
                           gp =
                           gpar(col = col.symbol, cex = cex, lwd = lwd,
                                alpha = alpha, fill = fill,
                                fontsize = fontsize.points,
                                fontfamily = fontfamily,
                                fontface = chooseFace(fontface, font), ...),
                           pch = pch, 
                           default.units = "native")
           },
           c = ,
           l = {
               grid.lines(x = x, y = y,
                          name = primName("lines", identifier, name.type, group),
                          gp = gpar(lty = lty, col = col.line, lwd = lwd, alpha = alpha, ...),
                          default.units = "native")
           },
           o = ,
           b = {
               grid.points(x = x, y = y, 
                           name = primName("points", identifier, name.type, group),
                           gp =
                           gpar(col = col.symbol, cex = cex, lwd = lwd,
                                alpha = alpha, fill = fill,
                                fontsize = fontsize.points,
                                fontfamily = fontfamily,
                                fontface = chooseFace(fontface, font), ...),
                           pch = pch, 
                           default.units = "native")
               grid.lines(x = x, y = y,
                          name = primName("lines", identifier, name.type, group),
                          gp = gpar(lty = lty, col = col.line, lwd = lwd, alpha = alpha, ...),
                          default.units = "native")
           },
           s = ,
           S = {
               ord <- seq_along(x) ## sort.list(x)
               if ((n <- length(x)) > 1)
               {
                   xx <- numeric(2*n-1)
                   yy <- numeric(2*n-1)
                   xx[2*1:n-1] <- x[ord]
                   yy[2*1:n-1] <- y[ord]
                   xx[2*1:(n-1)] <- x[ord][if (type=="s") -1 else -n]
                   yy[2*1:(n-1)] <- y[ord][if (type=="s") -n else -1]
                   grid.lines(x = xx, y = yy,
                              name = primName("lines", identifier, name.type, group),
                              gp = gpar(lty = lty, col = col.line, lwd = lwd, alpha = alpha, ...),
                              default.units="native")
               }
           },
           h = {
               ylim <- current.viewport()$yscale
               zero <-
                   if (min(ylim) > origin) min(ylim)
                   else if (max(ylim) < origin) max(ylim)
                   else origin
               grid.segments(x0 = x, x1 = x,
                             y0 = y, y1 = zero,
                             name = primName("segments", identifier, name.type, group),
                             gp =
                             gpar(lty = lty, col = col.line,
                                  lwd = lwd, alpha = alpha, ...),
                             default.units="native")
           },
           H = {
               xlim <- current.viewport()$xscale
               zero <-
                   if (min(xlim) > origin) min(xlim)
                   else if (max(xlim) < origin) max(xlim)
                   else origin
               grid.segments(x0 = x, x1 = zero,
                             y0 = y, y1 = y,
                             name = primName("segments", identifier, name.type, group),
                             gp =
                             gpar(lty = lty, col = col.line,
                                  lwd = lwd, alpha = alpha, ...),
                             default.units="native")
           })
##     if (type %in% c("l", "o", "b", "c"))
##         grid.lines(x = x, y = y,
##                    gp = gpar(lty = lty, col = col.line, lwd = lwd, alpha = alpha),
##                    default.units = "native")
##     else if (type %in% c("p", "o", "b", "c"))
##         grid.points(x = x, y = y, 
##                     gp =
##                     gpar(col = col, cex = cex,
##                          alpha = alpha, fill = fill,
##                          fontsize = fontsize.points,
##                          fontfamily = fontfamily,
##                          fontface = chooseFace(fontface, font)),
##                     pch = pch, 
##                     default.units = "native")
##     else if (type %in% c("s", "S"))
##     {
##         ord <- sort.list(x)
##         n <- length(x)
##         xx <- numeric(2*n-1)
##         yy <- numeric(2*n-1)
##         xx[2*1:n-1] <- x[ord]
##         yy[2*1:n-1] <- y[ord]
##         xx[2*1:(n-1)] <- x[ord][if (type=="s") -1 else -n]
##         yy[2*1:(n-1)] <- y[ord][if (type=="s") -n else -1]
##         grid.lines(x=xx, y=yy,
##                    gp = gpar(lty=lty, col=col.line, lwd=lwd, alpha = alpha),
##                    default.units="native")
##     }
##     else if (type == "h")
##     {
##         ylim <- current.viewport()$yscale
##         zero <-
##             if (ylim[1] > 0) ylim[1]
##             else if (ylim[2] < 0) ylim[2]
##             else 0
##         grid.segments(x0 = x, x1 = x,
##                       y0 = y, y1 = zero,
##                       gp =
##                       gpar(lty = lty, col = col.line,
##                            lwd = lwd, alpha = alpha),
##                       default.units="native")
##     }
##     else if (type == "H")
##     {
##         xlim <- current.viewport()$xscale
##         zero <-
##             if (xlim[1] > 0) xlim[1]
##             else if (xlim[2] < 0) xlim[2]
##             else 0
##         grid.segments(x0 = x, x1 = zero,
##                       y0 = y, y1 = y,
##                       gp =
##                       gpar(lty = lty, col = col.line,
##                            lwd = lwd, alpha = alpha),
##                       default.units="native")
##     }
    return()
}

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lattice documentation built on May 29, 2024, 7:29 a.m.