position_jitter_on_equal

DESCRIPTION

@@ -53,7 +53,7 @@ Imports:
     MASS,
     extrafont,
     plotly (>= 3.4.1)
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr
 Collate:
     'annotate_textp.r'
@@ -61,6 +61,7 @@ Collate:
     'formatters.r'
     'fortify.r'
     'position-dodgev.R'
+    'position-jitter-on-equal.R'
     'geom2plotly.r'
     'geom_ash.r'
     'geom_bkde.r'

NAMESPACE

@@ -22,6 +22,7 @@ export(GeomXspline)
 export(Kb)
 export(Mb)
 export(PositionDodgev)
+export(PositionJitterOnEqual)
 export(StatAsh)
 export(StatBkde)
 export(StatBkde2d)
@@ -44,6 +45,7 @@ export(geom_ubar)
 export(geom_xspline)
 export(load_stateface)
 export(position_dodgev)
+export(position_jitter_on_equal)
 export(show_stateface)
 export(stat_ash)
 export(stat_bkde)

R/geom_dumbbell.R

@@ -19,7 +19,10 @@
 #' @param shape_x,shape_xend shape to use for x/xend; defaults to 19
 #' @param fill_x,fill_xend fill for x/xend if the shape is hollow; defaults to fill aes
 #' @param dot_guide if \code{TRUE}, a leading dotted line will be placed before the left-most dumbbell point
-#' @param dot_guide_size,dot_guide_colour singe-value aesthetics for \code{dot_guide}
+#' @param dot_guide_size,dot_guide_colour singe-value ahesthetics for \code{dot_guide}
+#' @param jitter_on_equal_values numeric value [0..1], default is 0. If non-zero and if both
+#'        values are equal, jitter the points vertically by the amount specified so
+#'        they don't fully overlap.
 #' @param position Position adjustment, either as a string, or the result of a
 #'   call to a position adjustment function.
 #' @inheritParams ggplot2::layer
@@ -66,7 +69,7 @@ geom_dumbbell <- function(mapping = NULL, data = NULL, ...,
                           colour_x = NULL, size_x = NULL, shape_x = NULL, fill_x = NULL,
                           colour_xend = NULL, size_xend = NULL, shape_xend = NULL, fill_xend = NULL,
                           dot_guide = FALSE, dot_guide_size = NULL,
-                          dot_guide_colour = NULL,
+                          dot_guide_colour = NULL, jitter_on_equal_values = 0,
                           na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,
                           position = "identity") {
 
@@ -91,6 +94,7 @@ geom_dumbbell <- function(mapping = NULL, data = NULL, ...,
       dot_guide = dot_guide,
       dot_guide_size = dot_guide_size,
       dot_guide_colour = dot_guide_colour,
+      jitter_on_equal_values = jitter_on_equal_values,
       ...
     )
   )
@@ -105,23 +109,25 @@ GeomDumbbell <- ggproto("GeomDumbbell", Geom,
   non_missing_aes = c("size", "shape",
                       "colour_x", "size_x", "shape_x", "fill_x",
                       "colour_xend", "size_xend", "shape_xend", "fill_xend",
-                      "dot_guide", "dot_guide_size", "dot_guide_colour"),
+                      "dot_guide", "dot_guide_size", "dot_guide_colour",
+                      "jitter_on_equal_values"),
   default_aes = aes(
     shape = 19, colour = "black", size = 0.5, fill = NA,
     alpha = NA, stroke = 0.5
   ),
 
   setup_data = function(data, params) {
-    transform(data, yend = y)
+    transform(data, point_y = y, yend = y, dot_yend = y)
   },
 
   draw_group = function(data, panel_scales, coord,
                         colour_x = NULL, size_x = NULL, shape_x = NULL, fill_x = NULL,
                         colour_xend = NULL, size_xend = NULL, shape_xend = NULL, fill_xend = NULL,
                         dot_guide = NULL, dot_guide_size = NULL,
-                        dot_guide_colour = NULL) {
+                        dot_guide_colour = NULL, jitter_on_equal_values) {
 
     points.x <- data
+    points.x$y <- points.x$point_y
     points.x$colour <- colour_x %||% data$colour
     points.x$fill <- fill_x %||% data$fill
     points.x$shape <- shape_x %||% 19
@@ -129,6 +135,7 @@ GeomDumbbell <- ggproto("GeomDumbbell", Geom,
     points.x$size <- size_x %||% (data$size * 1.2)
 
     points.xend <- data
+    points.xend.y <- points.xend$yend
     points.xend$x <- points.xend$xend
     points.xend$colour <- colour_xend %||% data$colour
     points.xend$fill <- fill_xend %||% data$fill
@@ -139,6 +146,7 @@ GeomDumbbell <- ggproto("GeomDumbbell", Geom,
 
     dot_df <- data
     dot_df$xend <- ifelse(data$xend < data$x, data$xend, data$x)
+    dot_df$yend <- dot_df$dot_yend
     dot_df$x <- -Inf
     dot_df$linetype <- "11"
     dot_df$size <- dot_guide_size %||% (data$size * 0.5)
@@ -166,6 +174,7 @@ GeomDumbbell <- ggproto("GeomDumbbell", Geom,
   },
 
   draw_key = draw_key_point
+
 )
 
 

R/position-jitter-on-equal.R

@@ -0,0 +1,41 @@
+#' Jitter points to avoid overplotting
+#'
+#' Designed primarily for [geom_dumbbell()] to jitter the second point vertically
+#' when both x values are equal.
+#'
+#' @family position adjustments
+#' @param amount Amount of vertical jitter (0..1)
+#' @export
+position_jitter_on_equal <- function(amount = 0) {
+
+  ggproto(
+    NULL,
+    PositionJitterOnEqual,
+    amount = amount
+  )
+}
+
+#' @rdname ggplot2-ggproto
+#' @format NULL
+#' @usage NULL
+#' @export
+PositionJitterOnEqual <- ggproto(
+  "PositionJitterOnEqual", Position,
+  required_aes = c("x", "y"),
+
+  setup_params = function(self, data) {
+    list(
+      amount = self$amount
+    )
+  },
+
+  compute_layer = function(self, data, params, layout) {
+
+    data[data$x == data$xend,]$point_y <-
+      data[data$x == data$xend,]$point_y + (data[data$x == data$xend,]$point_y * params$amount)
+
+    data
+
+  }
+
+)

man/absoluteGrob.Rd

@@ -4,8 +4,14 @@
 \alias{absoluteGrob}
 \title{Absolute grob}
 \usage{
-absoluteGrob(grob, width = NULL, height = NULL, xmin = NULL,
-  ymin = NULL, vp = NULL)
+absoluteGrob(
+  grob,
+  width = NULL,
+  height = NULL,
+  xmin = NULL,
+  ymin = NULL,
+  vp = NULL
+)
 }
 \description{
 This grob has fixed dimensions and position.

man/annotate_textp.Rd

@@ -4,10 +4,22 @@
 \alias{annotate_textp}
 \title{Text annotations in plot coordinate system}
 \usage{
-annotate_textp(label, x, y, facets = NULL, hjust = 0, vjust = 0,
-  color = "black", alpha = NA, family = theme_get()$text$family,
-  size = theme_get()$text$size, fontface = 1, lineheight = 1,
-  box_just = ifelse(c(x, y) < 0.5, 0, 1), margin = unit(size/2, "pt"))
+annotate_textp(
+  label,
+  x,
+  y,
+  facets = NULL,
+  hjust = 0,
+  vjust = 0,
+  color = "black",
+  alpha = NA,
+  family = theme_get()$text$family,
+  size = theme_get()$text$size,
+  fontface = 1,
+  lineheight = 1,
+  box_just = ifelse(c(x, y) < 0.5, 0, 1),
+  margin = unit(size/2, "pt")
+)
 }
 \arguments{
 \item{label}{text annotation to be placed on the plot}
@@ -39,5 +51,5 @@ instead of data coordinates.
 \examples{
 p <- ggplot(mtcars, aes(x = wt, y = mpg)) + geom_point()
 p <- p + geom_smooth(method = "lm", se = FALSE)
-p + annotate_textp(x = 0.9, y = 0.35, label="A relative linear\\nrelationship", hjust=1, color="red")
+p + annotate_textp(x = 0.9, y = 0.35, label="A relative linear\nrelationship", hjust=1, color="red")
 }

man/annotation_ticks.Rd

@@ -4,10 +4,21 @@
 \alias{annotation_ticks}
 \title{Annotation: tick marks}
 \usage{
-annotation_ticks(sides = "b", scale = "identity", scaled = TRUE,
-  short = unit(0.1, "cm"), mid = unit(0.2, "cm"), long = unit(0.3,
-  "cm"), colour = "black", size = 0.5, linetype = 1, alpha = 1,
-  color = NULL, ticks_per_base = NULL, ...)
+annotation_ticks(
+  sides = "b",
+  scale = "identity",
+  scaled = TRUE,
+  short = unit(0.1, "cm"),
+  mid = unit(0.2, "cm"),
+  long = unit(0.3, "cm"),
+  colour = "black",
+  size = 0.5,
+  linetype = 1,
+  alpha = 1,
+  color = NULL,
+  ticks_per_base = NULL,
+  ...
+)
 }
 \arguments{
 \item{sides}{a string that controls which sides of the plot the log ticks appear on.

man/byte_format.Rd

@@ -16,8 +16,7 @@ Mb(x)
 
 Gb(x)
 
-bytes(x, symbol = "auto", units = c("binary", "si"),
-  only_highest = FALSE)
+bytes(x, symbol = "auto", units = c("binary", "si"), only_highest = FALSE)
 }
 \arguments{
 \item{symbol}{byte symbol to use. If "\code{auto}" the symbol used will be

man/geom_bkde.Rd

@@ -5,19 +5,39 @@
 \alias{stat_bkde}
 \title{Display a smooth density estimate.}
 \usage{
-geom_bkde(mapping = NULL, data = NULL, stat = "bkde",
-  position = "identity", bandwidth = NULL, range.x = NULL,
-  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
-
-stat_bkde(mapping = NULL, data = NULL, geom = "area",
-  position = "stack", kernel = "normal", canonical = FALSE,
-  bandwidth = NULL, gridsize = 410, range.x = NULL,
-  truncate = TRUE, na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE, ...)
+geom_bkde(
+  mapping = NULL,
+  data = NULL,
+  stat = "bkde",
+  position = "identity",
+  bandwidth = NULL,
+  range.x = NULL,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
+
+stat_bkde(
+  mapping = NULL,
+  data = NULL,
+  geom = "area",
+  position = "stack",
+  kernel = "normal",
+  canonical = FALSE,
+  bandwidth = NULL,
+  gridsize = 410,
+  range.x = NULL,
+  truncate = TRUE,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -25,11 +45,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -59,9 +79,9 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}

man/geom_bkde2d.Rd

@@ -5,20 +5,42 @@
 \alias{stat_bkde2d}
 \title{Contours from a 2d density estimate.}
 \usage{
-geom_bkde2d(mapping = NULL, data = NULL, stat = "bkde2d",
-  position = "identity", bandwidth = NULL, range.x = NULL,
-  lineend = "butt", contour = TRUE, linejoin = "round",
-  linemitre = 1, na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE, ...)
-
-stat_bkde2d(mapping = NULL, data = NULL, geom = "density2d",
-  position = "identity", contour = TRUE, bandwidth = NULL,
-  grid_size = c(51, 51), range.x = NULL, truncate = TRUE,
-  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
+geom_bkde2d(
+  mapping = NULL,
+  data = NULL,
+  stat = "bkde2d",
+  position = "identity",
+  bandwidth = NULL,
+  range.x = NULL,
+  lineend = "butt",
+  contour = TRUE,
+  linejoin = "round",
+  linemitre = 1,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
+
+stat_bkde2d(
+  mapping = NULL,
+  data = NULL,
+  geom = "density2d",
+  position = "identity",
+  contour = TRUE,
+  bandwidth = NULL,
+  grid_size = c(51, 51),
+  range.x = NULL,
+  truncate = TRUE,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -26,11 +48,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -73,9 +95,9 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}

man/geom_dumbbell.Rd

@@ -4,16 +4,31 @@
 \alias{geom_dumbbell}
 \title{Dumbbell charts}
 \usage{
-geom_dumbbell(mapping = NULL, data = NULL, ..., colour_x = NULL,
-  size_x = NULL, shape_x = NULL, fill_x = NULL, colour_xend = NULL,
-  size_xend = NULL, shape_xend = NULL, fill_xend = NULL,
-  dot_guide = FALSE, dot_guide_size = NULL, dot_guide_colour = NULL,
-  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,
-  position = "identity")
+geom_dumbbell(
+  mapping = NULL,
+  data = NULL,
+  ...,
+  colour_x = NULL,
+  size_x = NULL,
+  shape_x = NULL,
+  fill_x = NULL,
+  colour_xend = NULL,
+  size_xend = NULL,
+  shape_xend = NULL,
+  fill_xend = NULL,
+  dot_guide = FALSE,
+  dot_guide_size = NULL,
+  dot_guide_colour = NULL,
+  jitter_on_equal_values = 0,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  position = "identity"
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -21,11 +36,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -47,7 +62,11 @@ to the paired geom/stat.}
 
 \item{dot_guide}{if \code{TRUE}, a leading dotted line will be placed before the left-most dumbbell point}
 
-\item{dot_guide_size, dot_guide_colour}{singe-value aesthetics for \code{dot_guide}}
+\item{dot_guide_size, dot_guide_colour}{singe-value ahesthetics for \code{dot_guide}}
+
+\item{jitter_on_equal_values}{numeric value [0..1], default is 0. If non-zero and if both
+values are equal, jitter the points vertically by the amount specified so
+they don't fully overlap.}
 
 \item{na.rm}{If \code{FALSE} (the default), removes missing values with
 a warning.  If \code{TRUE} silently removes missing values.}
@@ -61,7 +80,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
 \item{position}{Position adjustment, either as a string, or the result of a
 call to a position adjustment function.}

man/geom_encircle.Rd

@@ -4,9 +4,16 @@
 \alias{geom_encircle}
 \title{Automatically enclose points in a polygon}
 \usage{
-geom_encircle(mapping = NULL, data = NULL, stat = "identity",
-  position = "identity", na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE, ...)
+geom_encircle(
+  mapping = NULL,
+  data = NULL,
+  stat = "identity",
+  position = "identity",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
 }
 \arguments{
 \item{mapping}{mapping}

man/geom_horizon.Rd

@@ -7,16 +7,34 @@
 \alias{stat_horizon}
 \alias{StatHorizon}
 \title{Plot a time series as a horizon plot}
-\format{An object of class \code{GeomHorizon} (inherits from \code{GeomArea}, \code{GeomRibbon}, \code{Geom}, \code{ggproto}, \code{gg}) of length 4.}
+\format{
+An object of class \code{GeomHorizon} (inherits from \code{GeomArea}, \code{GeomRibbon}, \code{Geom}, \code{ggproto}, \code{gg}) of length 4.
+
+An object of class \code{StatHorizon} (inherits from \code{Stat}, \code{ggproto}, \code{gg}) of length 5.
+}
 \usage{
-geom_horizon(mapping = NULL, data = NULL, show.legend = TRUE,
-  inherit.aes = TRUE, na.rm = TRUE, bandwidth = NULL, ...)
+geom_horizon(
+  mapping = NULL,
+  data = NULL,
+  show.legend = TRUE,
+  inherit.aes = TRUE,
+  na.rm = TRUE,
+  bandwidth = NULL,
+  ...
+)
 
 GeomHorizon
 
-stat_horizon(mapping = NULL, data = NULL, geom = "horizon",
-  show.legend = TRUE, inherit.aes = TRUE, na.rm = TRUE,
-  bandwidth = NULL, ...)
+stat_horizon(
+  mapping = NULL,
+  data = NULL,
+  geom = "horizon",
+  show.legend = TRUE,
+  inherit.aes = TRUE,
+  na.rm = TRUE,
+  bandwidth = NULL,
+  ...
+)
 
 StatHorizon
 }

man/geom_lollipop.Rd

@@ -4,13 +4,21 @@
 \alias{geom_lollipop}
 \title{Lollipop charts}
 \usage{
-geom_lollipop(mapping = NULL, data = NULL, ..., horizontal = FALSE,
-  point.colour = NULL, point.size = NULL, na.rm = FALSE,
-  show.legend = NA, inherit.aes = TRUE)
+geom_lollipop(
+  mapping = NULL,
+  data = NULL,
+  ...,
+  horizontal = FALSE,
+  point.colour = NULL,
+  point.size = NULL,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -18,11 +26,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -57,7 +65,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 }
 \description{
 The lollipop geom is used to create lollipop charts.

man/geom_spikelines.Rd

@@ -4,14 +4,23 @@
 \alias{geom_spikelines}
 \title{Draw spikelines on a plot}
 \usage{
-geom_spikelines(mapping = NULL, data = NULL, stat = "identity",
-  position = "identity", ..., arrow = NULL, lineend = "butt",
-  linejoin = "round", na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE)
+geom_spikelines(
+  mapping = NULL,
+  data = NULL,
+  stat = "identity",
+  position = "identity",
+  ...,
+  arrow = NULL,
+  lineend = "butt",
+  linejoin = "round",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -19,11 +28,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -36,7 +45,7 @@ layer, as a string.}
 \item{position}{Position adjustment, either as a string, or the result of
 a call to a position adjustment function.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}
@@ -59,7 +68,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 }
 \description{
 Segment reference lines that originate at an point

man/geom_stateface.Rd

@@ -4,14 +4,24 @@
 \alias{geom_stateface}
 \title{Use ProPublica's StateFace font in ggplot2 plots}
 \usage{
-geom_stateface(mapping = NULL, data = NULL, stat = "identity",
-  position = "identity", ..., parse = FALSE, nudge_x = 0,
-  nudge_y = 0, check_overlap = FALSE, na.rm = FALSE,
-  show.legend = NA, inherit.aes = TRUE)
+geom_stateface(
+  mapping = NULL,
+  data = NULL,
+  stat = "identity",
+  position = "identity",
+  ...,
+  parse = FALSE,
+  nudge_x = 0,
+  nudge_y = 0,
+  check_overlap = FALSE,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -19,11 +29,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -34,9 +44,10 @@ from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
 layer, as a string.}
 
 \item{position}{Position adjustment, either as a string, or the result of
-a call to a position adjustment function.}
+a call to a position adjustment function. Cannot be jointy specified with
+\code{nudge_x} or \code{nudge_y}.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}
@@ -49,7 +60,9 @@ abels by. Useful for offsetting text from points, particularly
 on discrete scales.}
 
 \item{check_overlap}{If \code{TRUE}, text that overlaps previous text in the
-same layer will not be plotted.}
+same layer will not be plotted. \code{check_overlap} happens at draw time and in
+the order of the data. Therefore data should be arranged by the label
+column before calling \code{geom_label()} or \code{geom_text()}.}
 
 \item{na.rm}{If \code{FALSE}, the default, missing values are removed with
 a warning. If \code{TRUE}, missing values are silently removed.}
@@ -63,7 +76,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 }
 \description{
 The \code{label} parameter can be either a 2-letter state abbreviation
@@ -114,7 +127,8 @@ gg
 }
 }
 \seealso{
-Other StateFace operations: \code{\link{load_stateface}},
-  \code{\link{show_stateface}}
+Other StateFace operations: 
+\code{\link{load_stateface}()},
+\code{\link{show_stateface}()}
 }
 \concept{StateFace operations}

man/geom_ubar.Rd

@@ -4,13 +4,20 @@
 \alias{geom_ubar}
 \title{Uniform "bar" charts}
 \usage{
-geom_ubar(mapping = NULL, data = NULL, stat = "identity",
-  position = "identity", ..., na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE)
+geom_ubar(
+  mapping = NULL,
+  data = NULL,
+  stat = "identity",
+  position = "identity",
+  ...,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -18,11 +25,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -52,7 +59,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 }
 \description{
 I've been using \code{geom_segment} more to make "bar" charts, setting

man/geom_xspline.Rd

@@ -5,19 +5,37 @@
 \alias{stat_xspline}
 \title{Connect control points/observations with an X-spline}
 \usage{
-geom_xspline(mapping = NULL, data = NULL, stat = "xspline",
-  position = "identity", na.rm = TRUE, show.legend = NA,
-  inherit.aes = TRUE, spline_shape = -0.25, open = TRUE,
-  rep_ends = TRUE, ...)
-
-stat_xspline(mapping = NULL, data = NULL, geom = "line",
-  position = "identity", na.rm = TRUE, show.legend = NA,
-  inherit.aes = TRUE, spline_shape = -0.25, open = TRUE,
-  rep_ends = TRUE, ...)
+geom_xspline(
+  mapping = NULL,
+  data = NULL,
+  stat = "xspline",
+  position = "identity",
+  na.rm = TRUE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  spline_shape = -0.25,
+  open = TRUE,
+  rep_ends = TRUE,
+  ...
+)
+
+stat_xspline(
+  mapping = NULL,
+  data = NULL,
+  geom = "line",
+  position = "identity",
+  na.rm = TRUE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  spline_shape = -0.25,
+  open = TRUE,
+  rep_ends = TRUE,
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -25,11 +43,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -51,7 +69,7 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
 \item{spline_shape}{A numeric vector of values between -1 and 1, which
 control the shape of the spline relative to the control points.}
@@ -63,7 +81,7 @@ closed shape.}
 first and last control points should be replicated for drawing the
 curve. Ignored for closed X-splines.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}
@@ -194,6 +212,7 @@ Blanc, C. and Schlick, C. (1995), "X-splines : A Spline Model
  \code{\link[graphics]{xspline}};
  \code{\link[grid]{grid.xspline}}
 
-Other xspline implementations: \code{\link{geom_xspline2}}
+Other xspline implementations: 
+\code{\link{geom_xspline2}()}
 }
 \concept{xspline implementations}

man/geom_xspline2.Rd

@@ -5,13 +5,20 @@
 \title{Alternative implemenation for connecting  control points/observations
 with an X-spline}
 \usage{
-geom_xspline2(mapping = NULL, data = NULL, stat = "identity",
-  position = "identity", na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE, ...)
+geom_xspline2(
+  mapping = NULL,
+  data = NULL,
+  stat = "identity",
+  position = "identity",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -19,11 +26,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -48,9 +55,9 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}
@@ -63,7 +70,8 @@ Alternative implemenation for connecting  control points/observations
 with an X-spline
 }
 \seealso{
-Other xspline implementations: \code{\link{geom_xspline}}
+Other xspline implementations: 
+\code{\link{geom_xspline}()}
 }
 \author{
 Ben Bolker

man/ggalt.Rd

@@ -3,7 +3,6 @@
 \docType{package}
 \name{ggalt}
 \alias{ggalt}
-\alias{ggalt-package}
 \title{Extra Geoms, Stats, Coords, Scales & Fonts for 'ggplot2'}
 \description{
 A package containing additional geoms, coords, stats, scales & fonts

man/ggplot2-ggproto.Rd

@@ -1,8 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/annotation_ticks.r
+% Please edit documentation in R/annotation_ticks.r,
+%   R/position-jitter-on-equal.R
 \docType{data}
 \name{GeomTicks}
 \alias{GeomTicks}
+\alias{PositionJitterOnEqual}
 \title{Base ggproto classes for ggplot2}
 \description{
 If you are creating a new geom, stat, position, or scale in another package,

man/load_stateface.Rd

@@ -11,7 +11,8 @@ Makes the ProPublica StateFace font available to PDF, PostScript,
 et. al. devices.
 }
 \seealso{
-Other StateFace operations: \code{\link{geom_stateface}},
-  \code{\link{show_stateface}}
+Other StateFace operations: 
+\code{\link{geom_stateface}()},
+\code{\link{show_stateface}()}
 }
 \concept{StateFace operations}

man/position_jitter_on_equal.Rd

@@ -0,0 +1,16 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/position-jitter-on-equal.R
+\name{position_jitter_on_equal}
+\alias{position_jitter_on_equal}
+\title{Jitter points to avoid overplotting}
+\usage{
+position_jitter_on_equal(amount = 0)
+}
+\arguments{
+\item{amount}{Amount of vertical jitter (0..1)}
+}
+\description{
+Designed primarily for [geom_dumbbell()] to jitter the second point vertically
+when both x values are equal.
+}
+\concept{position adjustments}

man/show_stateface.Rd

@@ -12,7 +12,8 @@ in the on-screen plot device for ggplot2, you need to install
 the font on your system
 }
 \seealso{
-Other StateFace operations: \code{\link{geom_stateface}},
-  \code{\link{load_stateface}}
+Other StateFace operations: 
+\code{\link{geom_stateface}()},
+\code{\link{load_stateface}()}
 }
 \concept{StateFace operations}

man/stat_ash.Rd

@@ -4,13 +4,24 @@
 \alias{stat_ash}
 \title{Compute and display a univariate averaged shifted histogram (polynomial kernel)}
 \usage{
-stat_ash(mapping = NULL, data = NULL, geom = "area",
-  position = "stack", ab = NULL, nbin = 50, m = 5, kopt = c(2,
-  2), na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
+stat_ash(
+  mapping = NULL,
+  data = NULL,
+  geom = "area",
+  position = "stack",
+  ab = NULL,
+  nbin = 50,
+  m = 5,
+  kopt = c(2, 2),
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -18,11 +29,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -58,9 +69,9 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}

man/stat_stepribbon.Rd

@@ -4,13 +4,21 @@
 \alias{stat_stepribbon}
 \title{Step ribbon statistic}
 \usage{
-stat_stepribbon(mapping = NULL, data = NULL, geom = "ribbon",
-  position = "identity", na.rm = FALSE, show.legend = NA,
-  inherit.aes = TRUE, direction = "hv", ...)
+stat_stepribbon(
+  mapping = NULL,
+  data = NULL,
+  geom = "ribbon",
+  position = "identity",
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE,
+  direction = "hv",
+  ...
+)
 }
 \arguments{
-\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
-\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+\item{mapping}{Set of aesthetic mappings created by \code{\link[ggplot2:aes]{aes()}} or
+\code{\link[ggplot2:aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
 default), it is combined with the default mapping at the top level of the
 plot. You must supply \code{mapping} if there is no plot mapping.}
 
@@ -18,11 +26,11 @@ plot. You must supply \code{mapping} if there is no plot mapping.}
 options:
 
 If \code{NULL}, the default, the data is inherited from the plot
-data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+data as specified in the call to \code{\link[ggplot2:ggplot]{ggplot()}}.
 
 A \code{data.frame}, or other object, will override the plot
 data. All objects will be fortified to produce a data frame. See
-\code{\link[=fortify]{fortify()}} for which variables will be created.
+\code{\link[ggplot2:fortify]{fortify()}} for which variables will be created.
 
 A \code{function} will be called with a single argument,
 the plot data. The return value must be a \code{data.frame}, and
@@ -46,12 +54,12 @@ display.}
 \item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
 rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
-the default plot specification, e.g. \code{\link[=borders]{borders()}}.}
+the default plot specification, e.g. \code{\link[ggplot2:borders]{borders()}}.}
 
 \item{direction}{\code{hv} for horizontal-veritcal steps, \code{vh} for
 vertical-horizontal steps}
 
-\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+\item{...}{Other arguments passed on to \code{\link[ggplot2:layer]{layer()}}. These are
 often aesthetics, used to set an aesthetic to a fixed value, like
 \code{colour = "red"} or \code{size = 3}. They may also be parameters
 to the paired geom/stat.}