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Add Profile Glyphs as a Scatterplot

Source: R/geom_profileglyph.R
geom_profileglyph.Rd

The profileglyph geom is used to plot multivariate data as profile glyphs (Chambers et al. 1983; duToit et al. 1986) in a scatterplot.

Usage

geom_profileglyph(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  cols = character(0L),
  width = 10,
  size = 1,
  colour.bar = NULL,
  colour.line = NULL,
  colour.grid = NULL,
  linewidth.line = 1,
  linewidth.bar = 1,
  linewidth.grid = 1,
  fill.bar = NULL,
  fill.gradient = NULL,
  flip.axes = FALSE,
  bar = TRUE,
  line = TRUE,
  mirror = TRUE,
  draw.grid = FALSE,
  show.legend = NA,
  repel = FALSE,
  repel.control = gglyph.repel.control(),
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

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(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "green" or size = 3. They may also be parameters to the paired geom/stat.

cols

Name of columns specifying the variables to be plotted in the glyphs as a character vector.

width

The width of the bars.

size

The size of glyphs.

colour.bar

The colour of bars.

colour.line

The colour of profile line(s).

colour.grid

The colour of the grid lines.

linewidth.line

The line width of the profile line(s)

linewidth.bar

The line width of the bars.

linewidth.grid

The line width of the grid lines.

fill.bar

The fill colour of the bars.

fill.gradient

The palette for gradient fill of the segments. See Details section of col_numeric() function in the scales package for available options.

flip.axes

logical. If TRUE, axes are flipped.

bar

logical. If TRUE, profile bars are plotted.

line

logical. If TRUE, profile line is plotted.

mirror

logical. If TRUE, mirror profile is plotted.

draw.grid

logical. If TRUE, grid points are plotted along the whiskers if all the variables specified in cols are of type factor. Default is FALSE.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

repel

logical. If TRUE, the glyphs are repel away from each other to avoid overlaps. Default is FALSE.

repel.control

A list of control settings for the repel algorithm. Ignored if repel = FALSE. See gglyph.repel.control for details on the various control parameters.

inherit.aes

If 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. borders().

Value

A geom layer.

Aesthetics

geom_pieglyph() understands the following aesthetics (required aesthetics are in bold):

  • x

  • y

  • alpha

  • colour

  • fill

  • group

See vignette("ggplot2-specs", package = "ggplot2") for further details on setting these aesthetics.

The following additional aesthetics are considered if repel = TRUE:

  • point.size

  • segment.linetype

  • segment.colour

  • segment.size

  • segment.alpha

  • segment.curvature

  • segment.angle

  • segment.ncp

  • segment.shape

  • segment.square

  • segment.squareShape

  • segment.inflect

  • segment.debug

See ggrepel examples page for further details on setting these aesthetics.

References

Chambers JM, Cleveland WS, Kleiner B, Tukey PA (1983). Graphical Methods for Data Analysis. Chapman and Hall/CRC, Boca Raton. ISBN 978-1-351-07230-4.

duToit SHC, Steyn AGW, Stumpf RH (1986). Graphical Exploratory Data Analysis, Springer Texts in Statistics. Springer-Verlag, New York. ISBN 978-1-4612-9371-2.

See also

profileglyphGrob

Other geoms: geom_dotglyph(), geom_metroglyph(), geom_pieglyph(), geom_starglyph(), geom_tileglyph()

Examples

# Scale the data
zs <- c("hp", "drat", "wt", "qsec", "vs", "am", "gear", "carb")
mtcars[ , zs] <- lapply(mtcars[ , zs], scales::rescale)

mtcars$cyl <- as.factor(mtcars$cyl)
mtcars$lab <- row.names(mtcars)

library(ggplot2)
theme_set(theme_bw())
options(ggplot2.discrete.colour = RColorBrewer::brewer.pal(8, "Dark2"))
options(ggplot2.discrete.fill = RColorBrewer::brewer.pal(8, "Dark2"))

ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Mapped fill + line
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Mapped fill + bar
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Mapped colour + bar and line
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Mapped colour + line
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Mapped colour + bar
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Bars with different fill + bar and line
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Bars with different fill + bar
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Bars with gradient fill + bar and line
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.gradient = "Greens",
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.gradient = "Blues",
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.gradient = "RdYlBu",
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.gradient = "viridis",
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Bars with gradient fill + bar
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.gradient = "Greens",
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.gradient = "Blues",
                    mirror = FALSE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.gradient = "RdYlBu",
                    flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    line = FALSE,
                    fill.gradient = "viridis",
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  0.8) +
  ylim(c(-0, 550))


# Faceted
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    alpha =  0.8) +
  ylim(c(-0, 550)) +
  facet_grid(. ~ cyl)


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    alpha =  0.8) +
  ylim(c(-0, 550)) +
  facet_grid(. ~ cyl)


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    alpha =  0.8) +
  ylim(c(-0, 550)) +
  facet_grid(. ~ cyl)


# Repel glyphs
ggplot(data = mtcars) +
  geom_point(aes(x = mpg, y = disp, colour = cyl)) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    alpha =  1, repel = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_point(aes(x = mpg, y = disp, colour = cyl)) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    line = FALSE, mirror = FALSE,
                    alpha =  1, repel = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_point(aes(x = mpg, y = disp, colour = cyl)) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 5, width = 1,
                    bar = FALSE, flip.axes = TRUE,
                    alpha =  1, repel = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_point(aes(x = mpg, y = disp, colour = cyl)) +
  geom_profileglyph(aes(x = mpg, y = disp, colour = cyl),
                    cols = zs, size = 5, width = 1,
                    mirror = FALSE, flip.axes = TRUE,
                    alpha =  1, repel = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_point(aes(x = mpg, y = disp)) +
  geom_profileglyph(aes(x = mpg, y = disp),
                    cols = zs, size = 5, width = 1,
                    fill.bar = RColorBrewer::brewer.pal(8, "Dark2"),
                    alpha =  1, repel = TRUE) +
  ylim(c(-0, 550))


rm(mtcars)
mtcars[ , zs] <- lapply(mtcars[ , zs], scales::rescale)

mtcars[ , zs] <- lapply(mtcars[, zs],
                        function(x) cut(x, breaks = 3,
                                        labels = c(1, 2, 3)))
mtcars[ , zs] <- lapply(mtcars[ , zs], as.factor)

mtcars$cyl <- as.factor(mtcars$cyl)
mtcars$lab <- row.names(mtcars)

# Grid lines (when bar = TRUE)
ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 3, width = 1,
                    alpha =  0.8, draw.grid = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, col = cyl),
                    cols = zs, size = 3, width = 1,
                    alpha =  0.8, draw.grid = TRUE) +
  ylim(c(-0, 550))


ggplot(data = mtcars) +
  geom_profileglyph(aes(x = mpg, y = disp, fill = cyl),
                    cols = zs, size = 3, width = 1,
                    fill.gradient = "Blues",
                    alpha =  0.8, draw.grid = TRUE) +
  ylim(c(-0, 550))