Package 'ggtrace' reference manual

Title:	Trace and Highlight Groups of Data Points
Description:	Provides 'ggplot2' geoms that allow groups of data points to be outlined or highlighted for emphasis. This is particularly useful when working with dense datasets that are prone to overplotting.
Authors:	Ryan Sheridan [aut, cre] , Rui Fu [ctb] , Jay Hesselberth [ctb] , RNA Bioscience Initiative [fnd, cph]
Maintainer:	Ryan Sheridan <[email protected]>
License:	MIT + file LICENSE
Version:	0.2.0.9000
Built:	2024-11-05 05:28:48 UTC
Source:	https://github.com/rnabioco/ggtrace

Each geom has an associated function that draws the key when the geom needs to be displayed in a legend. These functions are called draw_key_*(), where * stands for the name of the respective key glyph. The key glyphs can be customized for individual geoms by providing a geom with the key_glyph argument.

Usage

draw_key_point_trace(data, params, size)

draw_key_path_trace(data, params, size)
draw_key_point_trace(data, params, size)

draw_key_path_trace(data, params, size)

Arguments

`data`	A single row data frame containing the scaled aesthetics to display in this key
`params`	A list of additional parameters supplied to the geom.
`size`	Width and height of key in mm.

Value

A grid grob

Examples

p <- ggplot2::ggplot(stocks, ggplot2::aes(day, value, color = name))

# key glyphs can be specified by their name
p + ggplot2::geom_line(key_glyph = "point_trace")

# key glyphs can be specified via their drawing function
p + ggplot2::geom_line(key_glyph = ggplot2::draw_key_rect)

p <- ggplot2::ggplot(stocks, ggplot2::aes(day, value, color = name))

# key glyphs can be specified by their name
p + ggplot2::geom_line(key_glyph = "point_trace")

# key glyphs can be specified via their drawing function
p + ggplot2::geom_line(key_glyph = ggplot2::draw_key_rect)

Trace lines

Description

These geoms are similar to ggplot2::geom_path(), ggplot2::geom_line(), and ggplot2::geom_step(), but also include the ability to highlight line segments of interest. These geoms accept normal ggplot2 graphical parameters with some modifications. fill controls the color of the center line, color controls the outline color, and stroke controls outline width, similar to how filled shapes are modified for other ggplot2 geoms. Additional parameters including size, alpha, linetype, linejoin, lineend, and linemitre are also accepted.

Usage

geom_path_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  trace_position = "all",
  background_params = list(color = NA),
  lineend = "butt",
  linejoin = "round",
  linemitre = 10,
  arrow = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_line_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  orientation = NA,
  show.legend = NA,
  inherit.aes = TRUE,
  trace_position = "all",
  background_params = list(color = NA),
  ...
)

geom_step_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  direction = "hv",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  trace_position = "all",
  background_params = list(color = NA),
  ...
)
geom_path_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  trace_position = "all",
  background_params = list(color = NA),
  lineend = "butt",
  linejoin = "round",
  linemitre = 10,
  arrow = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_line_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  orientation = NA,
  show.legend = NA,
  inherit.aes = TRUE,
  trace_position = "all",
  background_params = list(color = NA),
  ...
)

geom_step_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  direction = "hv",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  trace_position = "all",
  background_params = list(color = NA),
  ...
)

Arguments

`mapping`	Set of aesthetic mappings created by `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, either as a `ggproto` `Geom` subclass or as a string naming the stat stripped of the `stat_` prefix (e.g. `"count"` rather than `"stat_count"`)
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`...`	Other arguments passed on to `layer()`. These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `size = 3`. They may also be parameters to the paired geom/stat.
`trace_position`	Specifies which data points to outline, can be one of: "all" to outline every group plotted A predicate specifying which data points to outline. This must evaluate to `TRUE` or `FALSE` within the context of the input data. e.g. `value > 100`
`background_params`	Named list specifying aesthetic parameters to use for background data points when a predicate is passed to `trace_position`, e.g. `list(color = "red")`
`lineend`	Line end style (round, butt, square).
`linejoin`	Line join style (round, mitre, bevel).
`linemitre`	Line mitre limit (number greater than 1).
`arrow`	Arrow specification, as created by `grid::arrow()`.
`na.rm`	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
`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.
`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()`.
`orientation`	The orientation of the layer. The default (`NA`) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting `orientation` to either `"x"` or `"y"`. See the Orientation section for more detail.
`direction`	direction of stairs: 'vh' for vertical then horizontal, 'hv' for horizontal then vertical, or 'mid' for step half-way between adjacent x-values.

Value

ggplot object

Aesthetics

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

x
y
alpha
colour
fill
group
linetype
size
stroke

Learn more about setting these aesthetics in vignette("ggplot2-specs").

Examples

# Modify line color for each group
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, fill = name)
) +
  geom_line_trace() +
  ggplot2::theme_minimal()

# Modify outline color for each group
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace() +
  ggplot2::theme_minimal()

# Specify outline color for each group
clrs <- c(
  CAC  = "#E69F00",
  DAX  = "#0072B2",
  FTSE = "#009E73",
  SMI  = "#56B4E9"
)

ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(stroke = 1) +
  ggplot2::scale_color_manual(values = clrs) +
  ggplot2::theme_minimal()

# Outline a subset of data points
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(trace_position = day > 1500, stroke = 1) +
  ggplot2::theme_minimal()

# Modify appearance of background data points
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(
    trace_position    = day > 1500,
    background_params = list(color = NA, fill = "grey75"),
    stroke            = 1
  ) +
  ggplot2::theme_minimal()

# Remove outline
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, fill = name)
) +
  geom_line_trace(
    trace_position    = day > 1500,
    background_params = list(fill = "grey75"),
    color             = NA
  ) +
  ggplot2::theme_minimal()

# Modify line color for each group
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, fill = name)
) +
  geom_line_trace() +
  ggplot2::theme_minimal()

# Modify outline color for each group
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace() +
  ggplot2::theme_minimal()

# Specify outline color for each group
clrs <- c(
  CAC  = "#E69F00",
  DAX  = "#0072B2",
  FTSE = "#009E73",
  SMI  = "#56B4E9"
)

ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(stroke = 1) +
  ggplot2::scale_color_manual(values = clrs) +
  ggplot2::theme_minimal()

# Outline a subset of data points
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(trace_position = day > 1500, stroke = 1) +
  ggplot2::theme_minimal()

# Modify appearance of background data points
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, color = name)
) +
  geom_line_trace(
    trace_position    = day > 1500,
    background_params = list(color = NA, fill = "grey75"),
    stroke            = 1
  ) +
  ggplot2::theme_minimal()

# Remove outline
ggplot2::ggplot(
  stocks,
  ggplot2::aes(day, value, fill = name)
) +
  geom_line_trace(
    trace_position    = day > 1500,
    background_params = list(fill = "grey75"),
    color             = NA
  ) +
  ggplot2::theme_minimal()

Trace points

Description

This geom is similar to ggplot2::geom_point(), but also includes the ability to outline points of interest. geom_point_trace() accepts normal ggplot2 graphical parameters with some modifications. fill controls the color of each point, color controls the outline color, and stroke controls outline width, similar to how filled shapes are modified for other ggplot2 geoms. Additional parameters including size, linetype, and alpha are also accepted.

Usage

geom_point_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  trace_position = "all",
  background_params = list(color = NA),
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)
geom_point_trace(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  trace_position = "all",
  background_params = list(color = NA),
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

`mapping`	Set of aesthetic mappings created by `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, either as a `ggproto` `Geom` subclass or as a string naming the stat stripped of the `stat_` prefix (e.g. `"count"` rather than `"stat_count"`)
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`...`	Other arguments passed on to `layer()`. These are often aesthetics, used to set an aesthetic to a fixed value, like `colour = "red"` or `size = 3`. They may also be parameters to the paired geom/stat.
`trace_position`	Specifies which data points to outline, can be one of: "all" to outline every group plotted "bottom" to only outline the bottom layer of data points A predicate specifying which data points to outline. This must evaluate to `TRUE` or `FALSE` within the context of the input data. e.g. `value > 100`
`background_params`	Named list specifying aesthetic parameters to use for background data points when a predicate is passed to `trace_position`, e.g. `list(color = "red")`
`na.rm`	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
`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.
`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

ggplot object

Aesthetics

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

x
y
alpha
colour
fill
group
linetype
shape
size
stroke

Learn more about setting these aesthetics in vignette("ggplot2-specs").

Examples

# Modify outline color for each group
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, color = cluster)
) +
  geom_point_trace() +
  ggplot2::theme_minimal()

# Outline a subset of points
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, fill = cluster)
) +
  geom_point_trace(trace_position = signal < 0 | signal > 17) +
  ggplot2::theme_minimal()

# Modify appearance of background points
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, fill = cluster)
) +
  geom_point_trace(
    trace_position    = signal < 0 | signal > 17,
    background_params = list(color = NA, fill = "grey85")
  ) +
  ggplot2::theme_minimal()

# Modify outline color for each group
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, color = cluster)
) +
  geom_point_trace() +
  ggplot2::theme_minimal()

# Outline a subset of points
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, fill = cluster)
) +
  geom_point_trace(trace_position = signal < 0 | signal > 17) +
  ggplot2::theme_minimal()

# Modify appearance of background points
ggplot2::ggplot(
  clusters,
  ggplot2::aes(UMAP_1, UMAP_2, fill = cluster)
) +
  geom_point_trace(
    trace_position    = signal < 0 | signal > 17,
    background_params = list(color = NA, fill = "grey85")
  ) +
  ggplot2::theme_minimal()

GeomPathTrace

Description

GeomPathTrace

Value

ggproto object

EuStockMarkets in long format

Description

EuStockMarkets in long format

Usage

stocks
stocks

Format

A tibble with 74440 rows and 3 variables

Package 'ggtrace'

Help Index

Mock clusters

Description

Usage

Format

Key glyphs for legends

Description

Usage

Arguments

Value

Examples

Trace lines

Description

Usage

Arguments

Value

Aesthetics

See Also

Examples

Trace points

Description

Usage

Arguments

Value

Aesthetics

See Also

Examples

GeomPathTrace

Description

Value

See Also

EuStockMarkets in long format

Description

Usage

Format