Type: Package
Title: Trace and Highlight Groups of Data Points
Version: 0.2.0
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.
License: MIT + file LICENSE
URL: https://github.com/rnabioco/ggtrace
BugReports: https://github.com/rnabioco/ggtrace/issues
Depends: R (≥ 4.0.0)
Imports: ggplot2, grid, rlang
Suggests: covr, knitr, rmarkdown, tidyr, tibble, dplyr, testthat (≥ 3.0.0), vdiffr (≥ 1.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.0
SystemRequirements: pandoc
Collate: 'a-legend-draw.R' 'data.R' 'geom-path-trace.R' 'geom-point-trace.R' 'ggtrace-package.R' 'grouping.R' 'utilities-ggplot2.R'
Config/Needs/website: pkgdown, rnabioco/rbitemplate
NeedsCompilation: no
Packaged: 2022-06-23 18:38:51 UTC; rmsheridan
Author: Ryan Sheridan ORCID iD [aut, cre], Rui Fu ORCID iD [ctb], Jay Hesselberth ORCID iD [ctb], RNA Bioscience Initiative [fnd, cph]
Maintainer: Ryan Sheridan <ryan.sheridan@cuanschutz.edu>
Repository: CRAN
Date/Publication: 2022-06-24 07:20:02 UTC

ggtrace

Description

This package 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.

Details

See the vignette for usage examples:

browseVignettes("ggtrace")

Author(s)

Ryan Sheridan ryan.sheridan@cuanschutz.edu

See Also

Report issues and suggest improvements at https://github.com/rnabioco/ggtrace/issues

GeomPathTrace

Description

GeomPathTrace

Value

ggproto object

See Also

GeomPath

Mock clusters

Description

Mock clusters

Usage

clusters

Format

A tibble with 14282 rows and 3 variables

Key glyphs for legends

Description

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)

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)

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),
  ...
)

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 = "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):

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

See Also

geom_path; geom_line; geom_step

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()

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
)

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 = "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):

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

See Also

geom_point

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()

EuStockMarkets in long format

Description

EuStockMarkets in long format

Usage

stocks

Format

A tibble with 74440 rows and 3 variables