geom_profileglyph: Add Profile Glyphs as a Scatterplot

In aravind-j/gglyph: Multivariate Data Visualization using Glyphs

Add Profile Glyphs as a Scatterplot

Description

The profileglyph geom is used to plot multivariate data as profile glyphs \insertCitechambers_graphical_1983,dutoit_graphical_1986gglyph 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

\insertAllCited

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))

aravind-j/gglyph documentation built on Aug. 2, 2022, 12:30 a.m.