Getting closer to passing R CMD check

DESCRIPTION

@@ -9,6 +9,7 @@ Description: An implementation of the grammar of graphics in R. It combines the
 Depends: R (>= 2.6), grid, reshape (>= 0.8.0), proto, splines, MASS,
   RColorBrewer, colorspace
 Suggests: quantreg, Hmisc, mapproj, maps, digest
+Imports: proto
 License: GPL
 URL: http://had.co.nz/ggplot2/
 LazyLoad: false

R/coordinates-cartesian-flipped.r

@@ -25,16 +25,16 @@ CoordFlipped <- proto(CoordCartesian, expr={
     # Very useful for creating boxplots, and other interval
     # geoms in the horizontal instead of vertical position.
     qplot(cut, price, data=diamonds, geom="boxplot")
-    .last_plot + coord_flip()
+    last_plot() + coord_flip()
 
     qplot(cut, data=diamonds, geom="bar")
-    .last_plot + coord_flip()
+    last_plot() + coord_flip()
 
     qplot(carat, data=diamonds, geom="histogram")
-    .last_plot + coord_flip()
+    last_plot() + coord_flip()
 
     # You can also use it to flip lines and area plots:
     qplot(1:5, (1:5)^2, geom="line")
-    .last_plot + coord_flip()
+    last_plot() + coord_flip()
   }
 })

R/matrix.r

@@ -4,10 +4,8 @@
 # @arguments data frame
 # @arguments any additional aesthetic mappings (do not use x and y)
 # @keyword hplot
-#X plotmatrix(mtcars)
-#X plotmatrix(mtcars, aes(colour=factor(cyl)))
-#X plotmatrix(mtcars) + geom_smooth(method="lm")
-#X plotmatrix(mtcars, aes(colour=factor(cyl))) 
+#X plotmatrix(mtcars[, 1:3])
+#X plotmatrix(mtcars[, 1:3]) + geom_smooth(method="lm")
 plotmatrix <- function(data, mapping=aes(), colour="black") {
   data <- rescaler(data, "range")
   grid <- expand.grid(x=1:ncol(data), y=1:ncol(data))
@@ -29,17 +27,17 @@ plotmatrix <- function(data, mapping=aes(), colour="black") {
   densities <- do.call("rbind", lapply(1:ncol(data), function(i) {
     data.frame(
       xvar = names(data)[i], 
-      yvar=names(data)[i],
+      yvar = names(data)[i],
       x = data[, i]
     )
   }))
-  mapping <- defaults(mapping, aes(x=x, y=y))
+  mapping <- defaults(mapping, aes_string(x="x", y="y"))
   class(mapping) <- "uneval"
 
   ggplot(all, mapping) + facet_grid(xvar ~ yvar) +
     geom_point(colour = colour) +
     scale_x_continuous("", limits=c(0, 1), breaks = seq(0,1, length=4), labels = "") +
     scale_y_continuous("", limits=c(0, 1), breaks = seq(0,1, length=4), labels = "") + 
-    stat_density(aes(x=x, y = ..scaled..), data=densities, position="identity", fill="grey60", colour=NA)
+    stat_density(aes_string(x="x", y = "..scaled.."), data=densities, position="identity", fill="grey60", colour=NA)
 }
 

R/options.r

@@ -158,4 +158,16 @@ update.ggplot <- function(object, ...) {
   if (length(dots) == 1 && is.list(dots[[1]])) dots <- dots[[1]]
 
   structure(defaults(dots, object), class="ggplot")
-}
+}
+
+.plot_store <- function() {
+  .last_plot <- NULL
+
+  list(
+    get = function() .last_plot, 
+    set = function(value) .last_plot <<- value
+  )
+}
+.store <- .plot_store()
+set_last_plot <- function(value) .store$set(value)
+last_plot <- function() .store$get()

R/plot-construction.r

@@ -37,5 +37,6 @@
     )
   }
   if (ggopt()$auto.print & length(p$layers) > 0) try(print(p))
-  (.last_plot <<- p)
+  set_last_plot(p)
+  p
 }

R/plot.r

@@ -24,7 +24,8 @@ ggplot.default <- function(data = NULL, mapping=aes(), ...) {
   p$facet <- FacetGrid$new()
   p$scales$add_defaults(p$data, p$defaults)
 
-  (.last_plot <<- p)
+  set_last_plot(p)
+  p
 }
 
 

R/save.r

@@ -26,7 +26,7 @@
 #X # make twice as big as on screen
 #X ggsave(ratings, file="ratings.pdf", scale=2)
 #X }
-ggsave <- function(plot = .last_plot, filename=default_name(plot), device=default_device(filename), scale=1, width=par("din")[1], height=par("din")[2], dpi=96, ...) {
+ggsave <- function(plot = last_plot(), filename=default_name(plot), device=default_device(filename), scale=1, width=par("din")[1], height=par("din")[2], dpi=96, ...) {
 
   ps <- function(..., width, height)  grDevices::ps(..., width=width, height=height)
   tex <- function(..., width, height) grDevices::pictex(..., width=width, height=height)

R/scale-continuous-.r

@@ -27,6 +27,7 @@ ScaleContinuous <- proto(Scale, {
   }
 
   train <- function(., x) {
+    if (is.null(x)) return()
     if (!is.numeric(x)) 
       warning("Non-numeric variable supplied to continuous scale ", .$name, ".", call.=FALSE)
     if (all(is.na(x))) return()

R/scales-.r

@@ -60,6 +60,8 @@ Scales <- proto(Scale, expr={
 
   # Train scale from a data frame
   train_df <- function(., df) {
+    if (is.null(df)) return()
+
     lapply(.$.scales, function(scale) {
       if (all(scale$input() %in% names(df))) scale$train_df(df)
     })

R/stat-sortx.r

@@ -4,7 +4,7 @@ StatSort <- proto(Stat, {
   default_geom <- function(.) GeomPath
 
   calculate_groups <- function(., data, scales, variable="x", ...) {
-    as.data.frame(data)[order(data$group, data$x[[variable]]), ]
+    as.data.frame(data)[order(data$group, data[[variable]]), ]
   }
   calculate <- calculate_groups
 

R/templates.r

@@ -41,7 +41,7 @@ ggpcp <- function(data, vars=names(data), scale="range", ...) {
   data$ROWID <- 1:nrow(data)
   molten <- melt(data, m=vars)
 
-  p <- ggplot(molten, aes(x=variable, y=value, group=ROWID), ...)
+  p <- ggplot(molten, aes_string(x="variable", y="value", group="ROWID"), ...)
   p + scale_x_discrete()
 }
 
@@ -88,9 +88,9 @@ ggfluctuation <- function(table, type="size", floor=0, ceiling=max(table$freq, n
   table <- subset(table, freq * ceiling >= floor)
 
   if (type=="size") {
-    p <- ggplot(table, aes(x=x, y=y, height=freq, width=freq, fill=border)) + geom_tile(colour="white") + scale_fill_identity()
+    p <- ggplot(table, aes_string(x="x", y="y", height="freq", width="freq", fill="border")) + geom_tile(colour="white") + scale_fill_identity()
   } else {
-    p <- ggplot(table, aes(x=x, y=y, fill=freq)) + 
+    p <- ggplot(table, aes_string(x="x", y="y", fill="freq")) + 
       geom_tile(colour="grey50") +
       scale_fill_gradient2(low="white", high="darkgreen")
   }
@@ -140,7 +140,7 @@ ggmissing <- function(data, avoid="stack", order=TRUE, missing.only = TRUE) {
     df$variable <- factor(df$variable)
   }
 
-  ggplot(df, aes(y=Freq, x=variable, fill=missing)) + geom_bar(position=avoid)
+  ggplot(df, aes_string(y="Freq", x="variable", fill="missing")) + geom_bar(position=avoid)
 }
 
 # Structure plot
@@ -152,7 +152,7 @@ ggmissing <- function(data, avoid="stack", order=TRUE, missing.only = TRUE) {
 #X ggstructure(mtcars)
 ggstructure <- function(data, scale = "rank") {
   ggpcp(data, scale=scale) + 
-    aes(y=ROWID, fill=value, x=variable) +
+    aes_string(y="ROWID", fill="value", x="variable") +
     geom_tile() +
     scale_y_continuous("row number", expand = c(0, 1)) +
     scale_fill_gradient2(low="blue", mid="white", high="red", midpoint=0)
@@ -166,7 +166,7 @@ ggstructure <- function(data, scale = "rank") {
 # @keyword hplot 
 ggorder <- function(data, scale="rank") {
   ggpcp(data, scale="rank") +
-    aes(x=ROWID, group=variable, y=value) +
+    aes_string(x="ROWID", group="variable", y="value") +
     facet_grid(. ~ variable) +
     geom_line() +
     scale_x_continuous("row number")
@@ -186,7 +186,7 @@ ggdist <- function(data, vars=names(data), facets = . ~ .) {
   mapply(function(name, cat, i) {
     p <- ggplot(data) + 
       facet_grid(facets) +
-      aes(x=as.name(name), y=1) +
+      aes_string(x=name, y=1) +
       geom_bar()
 
     pushViewport(viewport(layout.pos.col=i))

R/utilities-geoms.r

@@ -30,7 +30,7 @@ aes <- function(...) {
 # Generate aesthetic mappings from a string
 # Aesthetic mappings describe how variables in the data are mapped to visual properties (aesthetics) of geoms.  Compared to aes this function operates on strings rather than expressions.
 # 
-# aes_string is particularly useful when writing functions that create 
+# \code{aes_string} is particularly useful when writing functions that create 
 # plots because you can use strings to define the aesthetic mappings, rather
 # than having to mess around with expressions.
 #

R/weighting.r

@@ -17,11 +17,11 @@
 # qplot(wt, mpg, data=mtcars, weight=cyl, geom="wdensity", radius=1/20) # radius in proportion of data range, defaults to 1%
 # qplot(wt, mpg, data=mtcars, weight=cyl, geom="wdensity", trans=function(x) sqrt(x))
 # 
-# scalpha <- function(plot = .last_plot, name=NULL, colour="black", maxalpha=0.5) {
+# scalpha <- function(plot = last_plot(), name=NULL, colour="black", maxalpha=0.5) {
 #   add_scale(plot, scale_gradient(name=name, low=alpha(colour, 0), mid=alpha(colour, 0), high=alpha(colour, maxalpha), variable="weight", range=c(0,NA)))
 # }
 # 
-# scconserve <- function(plot = .last_plot, name=NULL, max=NA, colour="black", size.to = c(0.2, 5), alpha.to = c(1, 0)) {
+# scconserve <- function(plot = last_plot(), name=NULL, max=NA, colour="black", size.to = c(0.2, 5), alpha.to = c(1, 0)) {
 #   add_scale(plot, scale_conserve(name=name, max=max, colour=colour, size.to=size.to, alpha.to=alpha.to))
 # }
 # 
@@ -56,7 +56,7 @@
 # 
 # #sm.density(mtcars[,c("wt", "mpg")], display = "none", ngrid=200, h=c(0.1,0.1), eval.points=as.matrix((mtcars[,c("wt", "mpg")])))
 # 
-# ggwdensity <- function(plot = .last_plot, aes=aes(), ..., data=NULL) {
+# ggwdensity <- function(plot = last_plot(), aes=aes(), ..., data=NULL) {
 #   gg_add("wdensity", plot, aesthetics, ..., data=data)
 # }
 # 

man/aes-string-9e.rd

@@ -11,7 +11,7 @@ Aesthetic mappings describe how variables in the data are mapped to visual prope
 \item{...}{List of name value pairs}
 }
 
-\details{aes_string is particularly useful when writing functions that create
+\details{\code{aes_string} is particularly useful when writing functions that create
 plots because you can use strings to define the aesthetic mappings, rather
 than having to mess around with expressions.}
 \seealso{\code{\link{aes}}}

man/build-options-8a.rd

@@ -70,10 +70,9 @@ p # a very ugly plot!
 ggopt(background.fill = "white", background.color ="black")
 
 p <- qplot(wt, mpg, data=mtcars, colour=factor(cyl))
-p$legend.position <- c(0.9,0.9); p
-p$legend.position <- c(0.5,0.5)
-p$legend.justification <- "center"
-p
+p + opts(legend.position = c(0.9,0.9))
+(p <- p + opts(legend.position = c(0.5,0.5)))
+p + opts(legend.justification = "centre")
 
 DF <- data.frame(
 x=rnorm(20), 

man/ggaxis-60.rd

@@ -6,12 +6,13 @@
 \description{
 Grob for axes
 }
-\usage{ggaxis(at, labels, position="right", scale=c(0,1))}
+\usage{ggaxis(at, labels, position="right", scale=c(0,1), colour = ggopt()$axis.colour)}
 \arguments{
 \item{at}{position of ticks}
 \item{labels}{labels at ticks}
 \item{position}{position of axis (top, bottom, left or right)}
 \item{scale}{range of data values}
+\item{colour}{}
 }
 
 \details{}

man/ggsave-ao.rd

@@ -6,7 +6,7 @@
 \description{
 Save a ggplot with sensible defaults
 }
-\usage{ggsave(plot = .last_plot, filename=default_name(plot), device=default_device(filename), scale=1, width=par("din")[1], height=par("din")[2], dpi=96, ...)}
+\usage{ggsave(plot = last_plot(), filename=default_name(plot), device=default_device(filename), scale=1, width=par("din")[1], height=par("din")[2], dpi=96, ...)}
 \arguments{
 \item{plot}{plot to save, defaults to last plot displayed}
 \item{filename}{file name/path of plot}

man/ignore.rd

@@ -100,6 +100,7 @@
 \alias{nice_ramp}
 \alias{opts}
 \alias{pd}
+\alias{plist}
 \alias{plot_clone}
 \alias{PositionDodge}
 \alias{PositionFill}
@@ -140,10 +141,12 @@
 \alias{ScaleLog2}
 \alias{ScaleLogit}
 \alias{ScaleLog}
+\alias{ScaleManual}
 \alias{ScalePow10}
 \alias{ScalePower}
 \alias{ScaleProbability}
 \alias{ScaleProbit}
+\alias{ScaleReverse}
 \alias{ScaleShape}
 \alias{ScaleSizeDiscrete}
 \alias{ScaleSize}
@@ -158,6 +161,7 @@
 \alias{scale_colour_gradient}
 \alias{scale_colour_hue}
 \alias{scale_colour_identity}
+\alias{scale_colour_manual}
 \alias{scale_fill_brewer}
 \alias{scale_fill_colour}
 \alias{scale_fill_continuous}
@@ -166,12 +170,16 @@
 \alias{scale_fill_gradient}
 \alias{scale_fill_hue}
 \alias{scale_fill_identity}
+\alias{scale_fill_manual}
 \alias{scale_linetype_identity}
+\alias{scale_linetype_manual}
 \alias{scale_linetype}
 \alias{scale_shape_identity}
+\alias{scale_shape_manual}
 \alias{scale_shape}
 \alias{scale_size_discrete}
 \alias{scale_size_identity}
+\alias{scale_size_manual}
 \alias{scale_size}
 \alias{scale_xend_asn}
 \alias{scale_xend_atanh}
@@ -186,6 +194,7 @@
 \alias{scale_xend_pow}
 \alias{scale_xend_probit}
 \alias{scale_xend_prob}
+\alias{scale_xend_reverse}
 \alias{scale_xend_sqrt}
 \alias{scale_x_asn}
 \alias{scale_x_atanh}
@@ -202,6 +211,7 @@
 \alias{scale_x_pow}
 \alias{scale_x_probit}
 \alias{scale_x_prob}
+\alias{scale_x_reverse}
 \alias{scale_x_sqrt}
 \alias{scale_yend_asn}
 \alias{scale_yend_atanh}
@@ -216,6 +226,7 @@
 \alias{scale_yend_pow}
 \alias{scale_yend_probit}
 \alias{scale_yend_prob}
+\alias{scale_yend_reverse}
 \alias{scale_yend_sqrt}
 \alias{scale_y_asn}
 \alias{scale_y_atanh}
@@ -232,6 +243,7 @@
 \alias{scale_y_pow}
 \alias{scale_y_probit}
 \alias{scale_y_prob}
+\alias{scale_y_reverse}
 \alias{scale_y_sqrt}
 \alias{scale_z_asn}
 \alias{scale_z_atanh}
@@ -247,6 +259,7 @@
 \alias{scale_z_pow}
 \alias{scale_z_probit}
 \alias{scale_z_prob}
+\alias{scale_z_reverse}
 \alias{scale_z_sqrt}
 \alias{Scale}
 \alias{StatBin}
@@ -304,6 +317,7 @@
 \alias{TransLog}
 \alias{TransPow10}
 \alias{TransProbit}
+\alias{TransReverse}
 \alias{TransSqrt}
 \alias{Trans}
 \alias{try_require}
@@ -314,7 +328,8 @@
 \alias{ymedian}
 \alias{yrange}
 \alias{\%+\%}
-
+\alias{set_last_plot}
+\alias{last_plot}
 \keyword{hplot}
 \title{See website for documentation}
 \author{Hadley Wickham <h.wickham@gmail.com>}

man/plotmatrix-95.rd

@@ -15,8 +15,6 @@ Crude experimental scatterplot matrix
 
 \details{}
 
-\examples{plotmatrix(mtcars)
-plotmatrix(mtcars, aes(colour=factor(cyl)))
-plotmatrix(mtcars) + geom_smooth(method="lm")
-plotmatrix(mtcars, aes(colour=factor(cyl))) }
+\examples{plotmatrix(mtcars[, 1:3])
+plotmatrix(mtcars[, 1:3]) + geom_smooth(method="lm")}
 \keyword{hplot}