Ensure all geoms have correct legend type. Add set_scale_default func…

…tion

NEWS

@@ -1,33 +1,46 @@
+TODO for this release
+ * Complete rdoc documentation
+ * Profiling and some optimisations
+ * Multicolumn legends (and specification)
+
 ggplot 0.6
 ----------------------------------------
-
-  * fixed bug in combination of stat_bin and geom_area that made it difficult to draw frequency polygons
-  * coord_trans now deals with groups appropriately, at the cost of decreased speed
+  
+  * it's now easy to change the default scales (and their arguments) with the set_default_scale function, see ?set_default_scale for more details (thanks to Bob Muenchen for the suggestion)
+  * new order aesthetic which controls the order in which elements are plotted
   * min and max are now scaled the same way as y
   * functions are silently dropped (e.g. aes(colour=col))
-  * all size measurements (now lines and text as well) are measured in mm, lines/paths default to paths 0.5mm wide
-  * size legends resize to avoid overlaps
-  * preliminary legend merging code:
-     * consequence: legend type no longer specified in scale (e.g. size, identity, manual), but derived from geoms used
-  * fix scale adjustment bug in geom_density
-  * new geom_rug to add marginal rug plots
-  * all discrete scales now have labels argument which you can use to override the factor levels
-  * new stat_spoke to make it possible to use geom_segment parameterised by angle and radius (thanks to Jiho for the suggestion)
-  * new stat_function makes it easy to superimpose a function on the plot
-  * the middle line geom_crossbar is now display thicker than the other lines, controlled by the parameter fatten (thanks to Heike Hofmann for the suggestion)
-  * geom_vline, geom_hline and geom_abline should now behave better in a wider variety of settings
-  * convenient auto wrapping of simple summary functions for stat_sum
-  * better documentation for stat_sum
-  * na.rm added to the following statistics: stat_boxplot, stat_contour, stat_density2d, stat_qq, stat_density (thanks to Leena Choi for suggesting this)
-  * fixed bug in stat_bin which resulted in increased counts when the x axis was a categorical variable with a single level (thanks to Bob Muenchen for pointing this out!)
-  * fixed bug in geom_smooth where if se=FALSE x axis always includes 0
 
-Speed and documentation.  Profiling and complete rdoc documentation
+  * coord_polar: add start and direction parameters, giving more control over the layout of the polar coords
+  * coord_polar: added my favourite pie chart example
+  * coord_trans now deals with groups appropriately, at the cost of decreased speed
+  * geom_abline, geom_vline, geom_hline: should now behave better in a wider variety of settings
+  * geom_crossbar: the middle line is now display thicker than the other lines, controlled by the parameter fatten (thanks to Heike Hofmann for the suggestion)
+  * geom_density: fix scale adjustment bug in geom_density
+  * geom_line, geom_text: all size measurements (now lines and text as well) are measured in mm, lines/paths default to paths 0.5mm wide
+  * geom_rug: new to add marginal rug plots
+  * geom_smooth: fixed bug where if se=FALSE x axis always includes 0
+  * qplot: allow qplot to use computed aesthetics too
+  * scale_discrete: all discrete scales now have labels argument which you can use to override the factor levels
+  * scale_size: legends resize to avoid overlaps
+  * scale_x_continuous, scale_y_continuous: new convenience functions xlim and ylim (and zlim) that make it even easier to adjust the limits of the x, y, and z axes
+  * stat_bin, geom_area: fixed bug in combination of stat_bin and geom_area that made it difficult to draw frequency polygons
+  * stat_bin: fixed bug which resulted in increased counts when the x axis was a categorical variable with a single level (thanks to Bob Muenchen for pointing this out!)
+  * stat_bin: no longer incorrectly warns that binwidth is unspecified when breaks are set
+  * stat_bin: now takes origin argument to manually specify origin of first bin (default is round_any(min(range), bin_width, floor))
+  * stat_boxplot, stat_contour, stat_density2d, stat_qq, stat_density: na.rm parameter added to the following statistics (thanks to Leena Choi for suggesting this)
+  * stat_function: new, makes it easy to superimpose a function on the plot
+  * stat_spoke: new, to make it possible to use geom_segment parameterised by angle and radius (thanks to Jiho for the suggestion)
+  * stat_summary: better documentation
+  * stat_summary: convenient auto wrapping of simple summary functions
+
+Legends:
+
+  * preliminary legend merging code:
+   * consequence: legend type no longer specified in scale (e.g. size, identity, manual), but derived from geoms used
+   * better legends for smooth and pointrange
+   * fixed some examples where grob used instead of guide
 
-  * allow qplot to use computed aesthetics too
-  * add start and direction parameters to coord_polar, giving more control over the layout of the polar coords
-  * added my favourite pie chart example to coord_polar
-  * fixed some examples where grob used instead of guide
 
 Examples
 

R/geom-abline.r

@@ -32,6 +32,7 @@ GeomAbline <- proto(Geom, {
     geom_hline = "for horizontal lines",
     geom_vline = "for vertical lines"
   )
+  guide_geom <- function(.) "path"
 
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) c(GeomPath$default_aes(), aes(intercept = 0, slope = 1))

R/geom-hline.r

@@ -28,6 +28,7 @@ GeomHline <- proto(Geom, {
 
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) c(GeomPath$default_aes(), aes(intercept=0))
+  guide_geom <- function(.) "tile"
 
   seealso <- list(
     geom_vline = "for vertical lines",

R/geom-interval-bar.r

@@ -21,7 +21,7 @@ GeomBar <- proto(GeomInterval, {
     } else {
     with(data, 
       ggname(.$my_name(), rectGrob(x, max, width=width, height=max-min, default.units="native", just=c("centre", "top"), 
-      gp=gpar(col=colour, fill=fill, lwd=size * .pt, lty=linetype))
+      gp=gpar(col=colour, fill=fill, lwd=size * .pt, lty=linetype, lineend="butt"))
     ))
     }
 

R/geom-interval-crossbar.r

@@ -22,7 +22,8 @@ GeomCrossbar <- proto(GeomInterval, {
 
   default_stat <- function(.) StatIdentity
   default_pos <- function(.) PositionIdentity
-  default_aes = function(.) aes(colour="black", fill="NA", width=resolution(x) * 0.9, size=1, linetype=1, min=y, max=y)
+  default_aes = function(.) aes(colour="black", fill="NA", width=resolution(x) * 0.9, size=0.5, linetype=1, min=y, max=y)
+  guide_geom <- function(.) "path"
 
   draw <- function(., data, scales, coordinates, fatten = 2, ...) {
     ggname(.$my_name(), gTree(children=gList(

R/geom-interval-error.r

@@ -11,7 +11,7 @@ GeomErrorbar <- proto(GeomInterval, {
 
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) aes(colour = "black", size=0.5, linetype=1, width=0.9)
-  guide_geom <- function(.) "line"
+  guide_geom <- function(.) "path"
 
 
   seealso <- list(

R/geom-interval-line.r

@@ -11,7 +11,8 @@ GeomLinerange <- proto(GeomInterval, {
   )
 
   default_stat <- function(.) StatIdentity
-  default_aes <- function(.) aes(colour = "black", size=1, linetype=1)
+  default_aes <- function(.) aes(colour = "black", size=0.5, linetype=1)
+  guide_geom <- function(.) "path"
 
   draw <- function(., data, scales, coordinates, ...) {
     munched <- coordinates$transform(data)

R/geom-interval-point.r

@@ -17,6 +17,7 @@ GeomPointrange <- proto(GeomInterval, {
   )
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) aes(colour = "black", size=1, linetype=1, shape=19)
+  guide_geom <- function(.) "pointrange"
 
   draw <- function(., data, scales, coordinates, ...) {
     if (is.null(data$y)) return(GeomLinerange$draw(data, scales, coordinates, ...))
@@ -25,6 +26,16 @@ GeomPointrange <- proto(GeomInterval, {
       GeomPoint$draw(data, scales, coordinates, ...)
     )))
   }
+
+  draw_legend <- function(., data, ...) {
+    data <- aesdefaults(data, .$default_aes(), list(...))
+
+    gTree(children = gList(
+      GeomPath$draw_legend(data, ...),
+      GeomPoint$draw_legend(data, ...)
+    ))
+  }
+
 
   examples <- function(.) {
     # See geom_linerange for examples

R/geom-path-.r

@@ -3,9 +3,6 @@ GeomPath <- proto(Geom, {
 
   draw <- function(., data, scales, coordinates, ...) {
     if (nrow(data) < 2) return()
-
-    if (is.null(data$order)) data$order <- data$group
-    data <- data[order(data$order), ]
 
     munched <- coordinates$munch(data)
 
@@ -18,8 +15,7 @@ GeomPath <- proto(Geom, {
     n <- nrow(munched)
     group_diff <- munched$group[-1] != munched$group[-n]
     start <- c(TRUE, group_diff)
-    end <-   c(group_diff, TRUE)
-
+    end <-   c(group_diff, TRUE)  
 
     solid_lines <- all(sapply(g, function(df) identical(unique(df$linetype), 1)))
     constant <- all(sapply(g, function(df) nrow(unique(df[, c("colour","size","linetype")])) == 1))

R/geom-polygon.r

@@ -19,6 +19,7 @@ GeomPolygon <- proto(Geom, {
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) aes(colour="NA", fill="grey60", size=0.5, linetype=1)
   required_aes <- c("x", "y")
+  guide_geom <- function(.) "tile"
 
   seealso <- list(
     geom_path = "an unfilled polygon",

R/geom-quantile.r

@@ -5,6 +5,8 @@ GeomQuantile <- proto(GeomPath, {
   advice <- "<p>This can be used as a continuous analogue of a geom_boxplot.</p>\n"
   default_stat <- function(.) StatQuantile
   default_aes <- function(.) defaults(aes(weight=1, colour="grey50"), GeomPath$default_aes())
+  guide_geom <- function(.) "path"
+
 
   icon <- function(.) {
     ggname(.$my_name(), gTree(children=gList(

R/geom-ribbon-.r

@@ -15,7 +15,7 @@ GeomRibbon <- proto(GeomInterval, {
   }
 
   draw <- function(., data, scales, coordinates, ...) {
-    data <- subset(data, !is.na(x) & !is.na(y))
+    data <- data[complete.cases(data[, c("x","min","max")]), ]
     tb <- with(data,
       coordinates$munch(data.frame(x=c(x, rev(x)), y=c(max, rev(min))))
     )

R/geom-rug.r

@@ -29,6 +29,7 @@ GeomRug <- proto(Geom, {
 
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) aes(colour="black", size=0.5, linetype=1)
+  guide_geom <- function(.) "path"
 
   examples <- function(.) {
     p <- ggplot(mtcars, aes(x=wt, y=mpg))

R/geom-segment.r

@@ -35,6 +35,7 @@ GeomSegment <- proto(Geom, {
   default_stat <- function(.) StatIdentity
   required_aes <- c("x", "y", "xend", "yend")
   default_aes <- function(.) aes(colour="black", size=0.5, linetype=1)
+  guide_geom <- function(.) "path"
 
   examples <- function(.) {
     require("maps")

R/geom-smooth.r

@@ -16,11 +16,20 @@ GeomSmooth <- proto(GeomInterval, {
   }
 
   adjust_scales_data <- function(., scales, data) data
+  guide_geom <- function(.) "smooth"
 
   default_stat <- function(.) StatSmooth
   required_aes <- c("x", "y")
   default_aes <- function(.) aes(colour="grey50", fill=alpha("black", 0.2), size=0.5, linetype=1, weight=1)
 
+
+  draw_legend <- function(., data, ...) {
+    data <- aesdefaults(data, .$default_aes(), list(...))
+    gTree(children = gList(
+      GeomTile$draw_legend(data, ...),
+      GeomPath$draw_legend(data, ...)
+    ))
+  }
   examples <- function(.) {
     # See stat_smooth for examples
   }

R/geom-tile.r

@@ -25,13 +25,9 @@ GeomTile <- proto(Geom, {
   }
 
   draw_legend <- function(., data, ...)  {
-    data <- aesdefaults(data, list(colour=ggopt()$grid.fill, fill=NA), list(...))
-    if (all(is.na(data$fill))) {
-      data$fill <- data$colour
-      data$colour <- "grey50"
-    }
+    data <- aesdefaults(data, .$default_aes(), list(...))
 
-    rectGrob(gp=gpar(col=alpha(data$colour, 1), fill=alpha(data$fill, 1)))
+    rectGrob(gp=gpar(col=NA, fill=data$fill))
   }
 
   adjust_scales_data <- function(., scales, data) {

R/geom-vline.r

@@ -28,6 +28,7 @@ GeomVline <- proto(Geom, {
 
   default_stat <- function(.) StatIdentity
   default_aes <- function(.) c(GeomPath$default_aes(), aes(intercept=0))
+  guide_geom <- function(.) "path"
 
   seealso <- list(
     geom_hline = "for horizontal lines",

R/layer.r

@@ -170,6 +170,9 @@ Layer <- proto(expr = {
 
     check_required_aesthetics(.$geom$required_aes, c(names(data), names(.$geom_params)), paste("geom_", .$geom$objname, sep=""))
 
+    if (is.null(data$order)) data$order <- data$group
+    data <- data[order(data$order), ]
+
     do.call(.$geom$draw_groups, c(
       data = list(as.name("data")), 
       scales = list(as.name("scales")), 

R/scale-continuous-.r

@@ -130,3 +130,14 @@ ScaleContinuous <- proto(Scale, {
   }
 })
 
+xlim <- function(min=NA, max=NA) {
+  scale_x_continuous(limits = c(min, max))
+}
+
+ylim <- function(min=NA, max=NA) {
+  scale_y_continuous(limits = c(min, max))
+}
+
+zlim <- function(min=NA, max=NA) {
+  scale_z_continuous(limits = c(min, max))
+}

R/scale-defaults.r

@@ -0,0 +1,26 @@
+# Set default scale
+# Overrides the default scale with one of your choosing.
+#
+# @argument 
+# @argument type of variable (discrete, continuous, date)
+# @argument name of new default scale
+#X qplot(mpg, wt, data=mtcars, colour=factor(cyl)) 
+#X set_default_scale("colour","discrete", "grey")
+#X qplot(mpg, wt, data=mtcars, colour=factor(cyl)) 
+#X set_default_scale("colour","discrete", "hue")
+set_default_scale <- function(aesthetic, type, scale, ...) {
+  default <- paste("scale", aesthetic, type, sep="_")
+  settings <- list(...)
+
+  new_scale <- get(paste("Scale", firstUpper(scale), sep=""))
+  new_call <- function(...) {
+    do.call(new_scale$new, c(settings, list(..., variable=aesthetic)))
+  }
+  scale <- paste("scale", aesthetic, scale, sep="_")
+
+  # For development
+  if (exists(default, 1, inherits=FALSE)) {
+    assign(default, new_call, 1)
+  }
+  assignInNamespace(default, new_call, "ggplot2") 
+}

R/scale-discrete-.r

@@ -6,7 +6,7 @@ ScaleDiscrete <- proto(Scale, expr={
 
   train <- function(., x) {
     if (is.numeric(x)) {
-      warning("Numeric variable supplied to discrete scale ", .$name, ".", call.=FALSE) 
+      warning("Continuous variable (", .$name , ") supplied to ", .$my_name(), ", when a discrete variable was expected.  ", call.=FALSE) 
       .$.frange <- range(c(.$.frange, x), na.rm=TRUE)
     }
     .$.domain <- union(.$.domain, levels(x))

R/scale-discrete-colour.r

@@ -44,27 +44,27 @@ ScaleHue <- proto(ScaleColour, expr={
     (d <- qplot(carat, price, data=diamonds, colour=clarity))
 
     # Change scale label
-    d + scale_colour_discrete()
-    d + scale_colour_discrete("clarity")
-    d + scale_colour_discrete(expression(clarity[beta]))
+    d + scale_colour_hue()
+    d + scale_colour_hue("clarity")
+    d + scale_colour_hue(expression(clarity[beta]))
 
     # Adjust luminosity and chroma
-    d + scale_colour_discrete(l=40, c=30)
-    d + scale_colour_discrete(l=70, c=30)
-    d + scale_colour_discrete(l=70, c=150)
-    d + scale_colour_discrete(l=80, c=150)
+    d + scale_colour_hue(l=40, c=30)
+    d + scale_colour_hue(l=70, c=30)
+    d + scale_colour_hue(l=70, c=150)
+    d + scale_colour_hue(l=80, c=150)
 
     # Change range of hues used
-    d + scale_colour_discrete(h=c(0, 90))
-    d + scale_colour_discrete(h=c(90, 180))
-    d + scale_colour_discrete(h=c(180, 270))
-    d + scale_colour_discrete(h=c(270, 360))
+    d + scale_colour_hue(h=c(0, 90))
+    d + scale_colour_hue(h=c(90, 180))
+    d + scale_colour_hue(h=c(180, 270))
+    d + scale_colour_hue(h=c(270, 360))
 
     # Vary opacity
     # (only works with pdf, quartz and cairo devices)
-    d + scale_colour_discrete(alpha = 0.9)
-    d + scale_colour_discrete(alpha = 0.5)
-    d + scale_colour_discrete(alpha = 0.2)
+    d + scale_colour_hue(alpha = 0.9)
+    d + scale_colour_hue(alpha = 0.5)
+    d + scale_colour_hue(alpha = 0.2)
   }
 })
 ScaleColourDiscrete <- proto(ScaleHue, objname="discrete", doc=FALSE, examples=function(.) {})

R/scale-discrete-grey.r

@@ -1,8 +1,8 @@
 ScaleGrey <- proto(ScaleColour, expr={
   doc <- TRUE
 
-  new <- function(., name=NULL, variable, start = 0.3, end = 0.9, labels=NULL) {
-    .$proto(name=name, .input=variable, .output=variable, start=start, end=end, .lables = labels)
+  new <- function(., name=NULL, variable, start = 0.2, end = 0.8, labels=NULL) {
+    .$proto(name=name, .input=variable, .output=variable, start=start, end=end, .labels = labels)
   }
 
   breaks <- function(.) {