geom_text_pairwise: Label pairwise comparisons

In ggpp: Grammar Extensions to 'ggplot2'

Label pairwise comparisons

Description

Add a plot layer with a text label and a segment connecting two values along the x aesthetic. These are usually two levels of a factor mapped to the x aesthetic when used to report significance or highlighting pairwise comparisons.

Usage

geom_label_pairwise(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  nudge_x = 0,
  nudge_y = 0,
  default.colour = "black",
  default.color = default.colour,
  colour.target = "all",
  color.target = colour.target,
  default.alpha = 1,
  alpha.target = "segment",
  label.padding = grid::unit(0.25, "lines"),
  label.r = grid::unit(0.15, "lines"),
  segment.linewidth = 0.5,
  arrow = NULL,
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = FALSE
)

geom_text_pairwise(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  nudge_x = 0,
  nudge_y = 0,
  default.colour = "black",
  default.color = default.colour,
  colour.target = "all",
  color.target = colour.target,
  default.alpha = 1,
  alpha.target = "all",
  segment.linewidth = 0.5,
  arrow = NULL,
  check_overlap = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE
)

Arguments

mapping	Set of aesthetic mappings created by aes. With inherit.aes = FALSE (the default) it is not combined with the default mapping at the top level of the plot. You always need to supply a mapping unless you set inherit.aes = TRUE.
data	A data frame. If specified, overrides the default data frame defined at the top level of the plot.
stat	The statistical transformation to use on the data for this layer, as a string.
position	Position adjustment, either as a string, or the result of a call to a position adjustment function.
...	other arguments passed on to layer. There are three types of arguments you can use here: Aesthetics: to set an aesthetic to a fixed value, like colour = "red" or size = 3. Other arguments to the layer, for example you override the default stat associated with the layer. Other arguments passed on to the stat.
parse	If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.
nudge_x, nudge_y	Horizontal and vertical adjustments to nudge the starting position of each text label. The units for nudge_x and nudge_y are the same as for the data units on the x-axis and y-axis.
default.colour, default.color	A colour definition to use for elements not targeted by the colour aesthetic.
colour.target, color.target	A vector of character strings; "all", "text", "segment", "box", "box.line", and "box.fill" or "none".
default.alpha	numeric in [0..1] A transparency value to use for elements not targeted by the alpha aesthetic.
alpha.target	A vector of character strings; "all", "text", "segment", "box", "box.line", and "box.fill" or "none".
label.padding	Amount of padding around label. Defaults to 0.25 lines.
label.r	Radius of rounded corners. Defaults to 0.15 lines.
segment.linewidth	numeric Width of the segments or arrows in mm.
arrow	specification for arrow heads, as created by arrow
na.rm	If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.
show.legend	logical. Should this layer be included in the legends? NA includes a legend if any aesthetics are mapped. FALSE, the default, never includes it, and TRUE always includes it.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining them.
check_overlap	If TRUE, text that overlaps previous text in the same layer will not be plotted. check_overlap takes place at draw time and in the order of the data, thus its action depends of the size at which the plot is drawn.

Details

Geometries geom_text_pairwise() and geom_label_pairwise() have an interface similar to that of geom_text and geom_label, but add a segment connecting two values along x. In the most frequent use case they add a segment connecting pairs of levels from a grouping factor mapped to the x or y aesthetic. They can also be used to label ranges of values.

The segment extends from xmin to xmax, and the text label is located at x with a default that positions the label at the centre of the bar. The ends of the bar can be terminated with arrow heads given by parameter arrow, with a default of a plain segment without arrow tips. The text label is located slightly above the segment by the default value of vjust in geom_text_pairwise() and on top of the segment in geom_label_pairwise().

Layer functions geom_text_pairwise() and geom_label_pairwise() use by default position_nudge. Nudging affects both text label and bar, and its default of no displacement will very rarely need to be changed.

Differently to geom_text_repel() and geom_label_repel(), geom_text_pairwise() and geom_label_pairwise() do not make use of additional aesthetics for the segments or boxes, but instead allow the choice of which elements are targeted by the usual 'ggplot2' aesthetics and which are rendered using a default constant value. In the grammar of graphics using the same aesthetic with multiple meanings is not allowed, thus, the approach used in package 'ggpp' attempts to enforce this.

Value

A plot layer instance.

Under development!

This geometry is still under development and its user interface subject to change.

Plot boundaries and clipping

Note that when you change the scale limits for x and/or y of a plot, text labels stay the same size, as determined by the size aesthetic, given in millimetres. The actual size as seen in the plotted output is decided during the rendering of the plot to a graphics device. Limits are expanded only to include the anchor point of the labels because the "width" and "height" of a text element are 0 (as seen by ggplot2). Text labels do have height and width, but in grid units, not data units. Either function expand_limits or the scale expansion can be used to ensure text labels remain within the plotting area.

Alignment

You can modify text alignment with the vjust and hjust aesthetics. These can either be a number between 0 (right/bottom) and 1 (top/left) or a character ("left", "middle", "right", "bottom", "center", "top"). Values outside the range 0..1 displace the text label so that the anchor point is outside the text label. In addition, you can use special alignments for justification including "position", "inward" and "outward". Inward always aligns text towards the center of the plotting area, and outward aligns it away from the center of the plotting area. If tagged with _mean or _median (e.g., "outward_mean") the mean or median of the data in the panel along the corresponding axis is used as center. If the characters following the underscore represent a number (e.g., "outward_10.5") the reference point will be this value in data units. Position justification is computed based on the direction of the displacement of the position of the label so that each individual text or label is justified outwards from its original position. The default justification is "identity".

Aesthetics

Layer functions geom_text_pairwise() and geom_label_pairwise() require aesthetics xmin, xmax, x, y and label and support aesthetics: alpha, colour, group, size (of text), family, fontface, linewidth, linetype, hjust and vjust. In addition, geom_text_pairwise supports angle and geom_label_pairwise supports fill. See aes_colour_fill_alpha, aes_linetype_size_shape, aes_position, and aes_group_order.

In 'ggplot2' linewidth when applied to the border of the box drawn by geom_label() is given in points rather than in mm because of a historical error in the code. In other geometries such as geom_segment() linewidth is given in mm. As in geom_label_pairwise() it is important to remain consistent among different linewidth specifications, mm are used both for the box border and linking segment. To imitate the behaviour of geom_label() a correction factor of 0.75 (more exactly 1 pt = 0.7528 mm) can be used for the line width of the border of the box.

See Also

geom_text_s, geom_label_s, geom_text, geom_label and other documentation of package 'ggplot2'.

Examples

my.cars <- mtcars
my.cars$name <- rownames(my.cars)
p1 <- ggplot(my.cars, aes(factor(cyl), mpg)) +
       geom_boxplot(width = 0.33)

# With a factor mapped to x, highlight pairs

my.pairs <-
  data.frame(A = 1:2, B = 2:3, bar.height = c(12, 30),
             p.value = c(0.01, 0.05678))
p1 +
  geom_text_pairwise(data = my.pairs,
                     aes(xmin = A, xmax = B,
                         y = bar.height,
                         label = p.value),
                     parse = TRUE)

p1 +
  geom_text_pairwise(data = my.pairs,
                     aes(xmin = A, xmax = B,
                         y = bar.height,
                         label = sprintf("italic(P)~`=`~%.2f", p.value)),
                     arrow = grid::arrow(angle = 90,
                                         length = unit(1, "mm"),
                                         ends = "both"),
                     parse = TRUE)

p1 +
  geom_text_pairwise(data = my.pairs,
                     aes(xmin = A, xmax = B,
                         y = bar.height,
                         label = sprintf("italic(P)~`=`~%.2f", p.value)),
                     colour = "red",
                     arrow = grid::arrow(angle = 90,
                                         length = unit(1, "mm"),
                                         ends = "both"),
                     parse = TRUE)

p1 +
  geom_label_pairwise(data = my.pairs,
                      aes(xmin = A, xmax = B,
                          y = bar.height,
                          label = sprintf("italic(P)~`=`~%.2f", p.value)),
                      colour = "red", size = 2.75,
                      arrow = grid::arrow(angle = 30,
                                          length = unit(1.5, "mm"),
                                          ends = "both"),
                      parse = TRUE)

p1 +
  geom_text_pairwise(data = my.pairs,
                     aes(xmin = A, xmax = B,
                         y = bar.height,
                         label = sprintf("italic(P)~`=`~%.2f", p.value)),
                     colour = "red", colour.target = "segment",
                     arrow = grid::arrow(angle = 90,
                                         length = unit(1, "mm"),
                                         ends = "both"),
                     parse = TRUE)

p1 +
  geom_text_pairwise(data = my.pairs,
                     aes(xmin = A, xmax = B,
                         y = bar.height,
                         label = sprintf("italic(P)~`=`~%.2f", p.value)),
                     colour = "red", colour.target = "text",
                     arrow = grid::arrow(angle = 90,
                                         length = unit(1, "mm"),
                                         ends = "both"),
                     parse = TRUE)

# with a numeric vector mapped to x, indicate range

p2 <-
  ggplot(my.cars, aes(disp, mpg)) +
    geom_point()

my.ranges <-
  data.frame(A = c(50, 400),
             B = c(200, 500),
             bar.height = 5,
             text = c("small", "large"))

p2 +
  geom_text_pairwise(data = my.ranges,
                     aes(xmin = A, xmax = B,
                     y = bar.height, label = text))

p2 +
  geom_text_pairwise(data = my.ranges,
                     aes(xmin = A, xmax = B,
                         y = bar.height, label = text),
                     angle = 90, hjust = -0.1)

p2 +
  geom_label_pairwise(data = my.ranges,
                      aes(xmin = A, xmax = B,
                          y = bar.height, label = text),
                     angle = 90, hjust = -0.1)

p2 +
  geom_label_pairwise(data = my.ranges,
                      aes(xmin = A, xmax = B,
                          y = bar.height, label = text))

p2 +
  geom_text_pairwise(data = my.ranges,
                     aes(xmin = A, xmax = B,
                         y = bar.height, label = text),
                     arrow = grid::arrow(ends = "both", length = unit(2, "mm")))

ggpp documentation built on Nov. 8, 2023, 1:10 a.m.