Package 'ggalign'

Description

These settings control the behavior of the plot when added to a layout, as well as the arrangement of individual plot areas within the layout.

Usage

active(order = waiver(), use = waiver(), name = waiver())

Arguments

Details

By default, the active context is set only for functions that add plot areas. This allows other ggplot2 elements-such as geoms, stats, scales, or themes- to be seamlessly added to the current plot area.

The default ordering of the plot areas is from top to bottom or from left to right, depending on the layout orientation. However, users can customize this order using the order argument.

Description

This function aligns observations within the layout according to a hierarchical clustering tree, enabling reordering or grouping of elements based on clustering results.

Usage

align_dendro(
  mapping = aes(),
  ...,
  distance = "euclidean",
  method = "complete",
  use_missing = "pairwise.complete.obs",
  reorder_dendrogram = FALSE,
  merge_dendrogram = FALSE,
  reorder_group = FALSE,
  k = NULL,
  h = NULL,
  cutree = NULL,
  plot_dendrogram = TRUE,
  plot_cut_height = NULL,
  root = NULL,
  center = FALSE,
  type = "rectangle",
  size = NULL,
  data = NULL,
  no_axes = NULL,
  active = NULL,
  free_guides = deprecated(),
  free_spaces = deprecated(),
  plot_data = deprecated(),
  theme = deprecated(),
  free_labs = deprecated(),
  set_context = deprecated(),
  order = deprecated(),
  name = deprecated()
)

Arguments

Value

A "AlignDendro" object.

ggplot2 specification

align_dendro initializes a ggplot data and mapping.

The internal will always use a default mapping of aes(x = .data$x, y = .data$y).

The default ggplot data is the node coordinates with edge data attached in ggalign attribute, in addition, a geom_segment layer with a data of the edge coordinates will be added.

node and tree segments edge coordinates contains following columns:

• index: the original index in the tree for the current node

• label: node label text

• x and y: x-axis and y-axis coordinates for current node or the start node of the current edge.

• xend and yend: the x-axis and y-axis coordinates of the terminal node for current edge.

• branch: which branch current node or edge is. You can use this column to color different groups.

• panel: which panel current node is, if we split the plot into panel using facet_grid, this column will show which panel current node or edge is from. Note: some nodes may fall outside panel (between two panel), so there are possible NA values in this column.

• .panel: Similar with panel column, but always give the correct branch for usage of the ggplot facet.

• panel1 and panel2: The panel1 and panel2 variables have the same functionality as panel, but they are specifically for the edge data and correspond to both nodes of each edge.

• leaf: A logical value indicates whether current node is a leaf.

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

See Also

• dendrogram_data()

• hclust2()

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    align_dendro()
ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    align_dendro(k = 3L)

Description

align_gg() is similar to ggplot in that it initializes a ggplot data and mapping. Same with other ⁠align_*⁠ functions. align_gg() allowing you to provide data in various formats, including matrices, data frames, or simple vectors. By default, it will inherit from the layout. If a function, it will apply with the layout matrix. ggalign is an alias of align_gg.

Usage

align_gg(
  mapping = aes(),
  size = NULL,
  data = waiver(),
  limits = TRUE,
  facet = TRUE,
  no_axes = NULL,
  active = NULL,
  set_context = deprecated(),
  order = deprecated(),
  name = deprecated(),
  free_guides = deprecated(),
  free_spaces = deprecated(),
  plot_data = deprecated(),
  theme = deprecated(),
  free_labs = deprecated()
)

Arguments

Value

A "AlignGG" object.

ggplot2 specification

align_gg initializes a ggplot data and mapping.

align_gg() always applies a default mapping for the axis of the data index in the layout. This mapping is aes(y = .data$.y) for horizontal stack layout (including left and right annotation) and aes(x = .data$.x) for vertical stack layout (including top and bottom annotation).

matrix input will be automatically melted into a long foramted data frame.

Atomic vector will be put in the value column of the data frame.

In the case where the input data is already a data frame, 4 additional columns (.x/.y, .names, .index, and .panel) are added to the data frame.

The data in the underlying ggplot object will contain following columns:

• .panel: the panel for the aligned axis. It means x-axis for vertical stack layout (including top and bottom annotation), y-axis for horizontal stack layout (including left and right annotation).

• .x or .y: the x or y coordinates

• .names (vec_names()) and .index (vec_size()/NROW()): A factor of the names (only applicable when names exists) and an integer of index of the original data.

• .row_names and .row_index: the row names and an integer of row index of the original matrix (only applicable if data is a matrix).

• .column_names and .column_index: the column names and column index of the original matrix (only applicable if data is a matrix).

• value: the actual value (only applicable if data is a matrix or atomic vector).

It is recommended to use .x/.y, or .names as the x/y mapping.

If the data inherits from quad_layout()/ggheatmap(), an additional column will be added.

• .extra_panel: the panel information for column (left or right annotation) or row (top or bottom annotation).

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    ggalign() +
    geom_point(aes(y = value))

# if data is `NULL`, a three column data frame will be created
# (`.panel`, `.index`, `.x`/`.y`)
ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top(size = 0.5) +
    align_dendro(k = 3L) +
    ggalign(data = NULL, size = 0.2) +
    geom_tile(aes(y = 1L, fill = .panel))

Description

Splits observations into groups, with slice ordering based on group levels.

Usage

align_group(
  group,
  active = NULL,
  set_context = deprecated(),
  name = deprecated()
)

Arguments

Value

A "AlignGroup" object.

Examples

set.seed(1L)
small_mat <- matrix(rnorm(81), nrow = 9)
ggheatmap(small_mat) +
    anno_top() +
    align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))

Description

Aligns and groups observations based on k-means clustering, enabling observation splits by cluster groups.

Usage

align_kmeans(
  centers,
  ...,
  data = NULL,
  active = NULL,
  set_context = deprecated(),
  name = deprecated()
)

Arguments

Value

A "AlignKmeans" object.

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    align_kmeans(3L)

Description

Ordering observations based on summary weights or a specified ordering character or integer index.

Usage

align_order(
  weights = rowMeans,
  ...,
  reverse = FALSE,
  strict = TRUE,
  data = NULL,
  active = NULL,
  set_context = deprecated(),
  name = deprecated()
)

Arguments

Value

A "AlignOrder" object.

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_left() +
    align_order(I("rowMeans"))

Description

Arrange multiple plots into a grid

Usage

align_plots(
  ...,
  ncol = NULL,
  nrow = NULL,
  byrow = TRUE,
  widths = NA,
  heights = NA,
  design = NULL,
  guides = waiver(),
  theme = NULL
)

Arguments

Value

An alignpatches object.

See Also

• layout_design()

• layout_title()

• layout_annotation()

Examples

# directly copied from patchwork
p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p3 <- ggplot(mtcars) +
    geom_bar(aes(gear)) +
    facet_wrap(~cyl)
p4 <- ggplot(mtcars) +
    geom_bar(aes(carb))
p5 <- ggplot(mtcars) +
    geom_violin(aes(cyl, mpg, group = cyl))

# Either add the plots as single arguments
align_plots(p1, p2, p3, p4, p5)

# Or use bang-bang-bang to add a list
align_plots(!!!list(p1, p2, p3), p4, p5)

# Match plots to areas by name
design <- "#BB
           AA#"
align_plots(B = p1, A = p2, design = design)

# Compare to not using named plot arguments
align_plots(p1, p2, design = design)

Description

Reorders layout observations based on specific statistics.

Usage

align_reorder(
  stat,
  ...,
  reverse = FALSE,
  strict = TRUE,
  data = NULL,
  active = NULL,
  set_context = deprecated(),
  name = deprecated()
)

Arguments

Details

The align_reorder() function differs from align_order() in that the wts argument in align_order() must return atomic weights for each observation. In contrast, the stat argument in align_reorder() can return more complex structures, such as hclust or dendrogram, among others.

Typically, you can achieve the functionality of align_reorder() using align_order() by manually extracting the ordering information from the statistic.

Value

A "AlignReorder" object.

Axis Alignment for Observations

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

• quad_layout()/ggheatmap(): For column annotation, the layout matrix will be transposed before use (if data is a function, it is applied to the transposed matrix), as column annotation uses columns as observations but alignment requires rows.

• stack_layout(): The layout matrix is used as is, aligning all plots along a single axis.

See Also

order2()

Examples

ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_left() +
    align_reorder(hclust2)

Description

This is a small helper used to specify a single area in a rectangular grid that should contain a plot. Objects constructed with area() can be concatenated together with c() in order to specify multiple areas.

Usage

area(t, l, b = t, r = l)

Arguments

Details

The grid that the areas are specified in reference to enumerate rows from top to bottom, and coloumns from left to right. This means that t and l should always be less or equal to b and r respectively. Instead of specifying area placement with a combination of area() calls, it is possible to instead pass in a single string

areas <- c(area(1, 1, 2, 1),
           area(2, 3, 3, 3))

is equivalent to

areas < -"A##
          A#B
          ##B"

Value

A ggalign_area object.

Examples

p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p3 <- ggplot(mtcars) +
    geom_bar(aes(gear)) +
    facet_wrap(~cyl)

layout <- c(
    area(1, 1),
    area(1, 3, 3),
    area(3, 1, 3, 2)
)

# Show the layout to make sure it looks as it should
plot(layout)

# Apply it to a alignpatches
align_plots(p1, p2, p3, design = layout)

Description

Dengrogram x and y coordinates

Usage

dendrogram_data(
  tree,
  priority = "right",
  center = FALSE,
  type = "rectangle",
  leaf_pos = NULL,
  leaf_braches = NULL,
  reorder_branches = TRUE,
  branch_gap = NULL,
  root = NULL
)

Arguments

Value

A list of 2 data.frame. One for node coordinates, another for edge coordinates. node and tree segments edge coordinates contains following columns:

• index: the original index in the tree for the current node

• label: node label text

• x and y: x-axis and y-axis coordinates for current node or the start node of the current edge.

• xend and yend: the x-axis and y-axis coordinates of the terminal node for current edge.

• branch: which branch current node or edge is. You can use this column to color different groups.

• panel: which panel current node is, if we split the plot into panel using facet_grid, this column will show which panel current node or edge is from. Note: some nodes may fall outside panel (between two panels), so there are possible NA values in this column.

• .panel: Similar with panel column, but always give the correct branch for usage of the ggplot facet.

• panel1 and panel2: The panel1 and panel2 variables have the same functionality as panel, but they are specifically for the edge data and correspond to both nodes of each edge.

• leaf: A logical value indicates whether current node is a leaf.

Examples

dendrogram_data(hclust(dist(USArrests), "ave"))

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. The draw_key_draw function provides this interface for custom key glyphs used with geom_draw().

Usage

draw_key_draw(data, params, size)

Arguments

Value

A grid grob.

Examples

p <- ggplot(economics, aes(date, psavert, color = "savings rate"))
# key glyphs can be specified by their name
p + geom_line(key_glyph = "timeseries")

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

Description

This function converts various objects to a data frame.

Usage

fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

• fortify_data_frame.default()

• fortify_data_frame.character()

• fortify_data_frame.numeric()

• fortify_data_frame.matrix()

Description

When data is an atomic vector, it'll be converted to a data frame with following columns:

• .names: the names for the vector (only applicable if names exist).

• value: the actual value of the vector.

Usage

## S3 method for class 'character'
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.complex(), fortify_data_frame.default(), fortify_data_frame.logical(), fortify_data_frame.matrix(), fortify_data_frame.numeric()

Description

When data is an atomic vector, it'll be converted to a data frame with following columns:

• .names: the names for the vector (only applicable if names exist).

• value: the actual value of the vector.

Usage

## S3 method for class 'complex'
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.character(), fortify_data_frame.default(), fortify_data_frame.logical(), fortify_data_frame.matrix(), fortify_data_frame.numeric()

Description

By default, it calls fortify() to build the data frame.

Usage

## Default S3 method:
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.character(), fortify_data_frame.complex(), fortify_data_frame.logical(), fortify_data_frame.matrix(), fortify_data_frame.numeric()

Description

When data is an atomic vector, it'll be converted to a data frame with following columns:

• .names: the names for the vector (only applicable if names exist).

• value: the actual value of the vector.

Usage

## S3 method for class 'logical'
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.character(), fortify_data_frame.complex(), fortify_data_frame.default(), fortify_data_frame.matrix(), fortify_data_frame.numeric()

Description

When data is a matrix, it will automatically be transformed into a long-form data frame, where each row represents a unique combination of matrix indices and their corresponding values.

Usage

## S3 method for class 'matrix'
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.character(), fortify_data_frame.complex(), fortify_data_frame.default(), fortify_data_frame.logical(), fortify_data_frame.numeric()

Description

When data is an atomic vector, it'll be converted to a data frame with following columns:

• .names: the names for the vector (only applicable if names exist).

• value: the actual value of the vector.

Usage

## S3 method for class 'numeric'
fortify_data_frame(data, ...)

Arguments

Value

A data frame.

See Also

Other fortify_data_frame methods: fortify_data_frame.character(), fortify_data_frame.complex(), fortify_data_frame.default(), fortify_data_frame.logical(), fortify_data_frame.matrix()

Description

This function converts various objects into a matrix format.

Usage

fortify_matrix(data, ...)

Arguments

Value

A matrix.

See Also

• fortify_matrix.default()

• fortify_matrix.MAF()

• fortify_matrix.GISTIC()

Description

By default, it calls as.matrix() to build a matrix.

Usage

## Default S3 method:
fortify_matrix(data, ...)

Arguments

Value

A matrix.

See Also

Other fortify_matrix methods: fortify_matrix.GISTIC(), fortify_matrix.MAF()

Description

This function converts various objects into a matrix format.

Usage

## S3 method for class 'GISTIC'
fortify_matrix(
  data,
  ...,
  n_top = NULL,
  bands = NULL,
  ignored_bands = NULL,
  sample_anno = NULL,
  remove_empty_samples = TRUE
)

Arguments

Value

A matrix.

ggalign attributes

• sample_anno: sample clinical informations provided in sample_anno.

• sample_summary: sample copy number summary informations. See [email protected] for details.

• cytoband_summary: cytoband summary informations. See [email protected] for details.

• gene_summary: gene summary informations. See [email protected] for details.

• summary: A data frame of summary information. See data@summary for details.

See Also

Other fortify_matrix methods: fortify_matrix.MAF(), fortify_matrix.default()

Description

This function converts various objects into a matrix format.

Usage

## S3 method for class 'MAF'
fortify_matrix(
  data,
  ...,
  genes = NULL,
  n_top = NULL,
  remove_empty_samples = TRUE,
  collapse_vars = TRUE,
  use_syn = TRUE
)

Arguments

Value

A matrix.

ggalign attributes

• gene_summary: gene summary informations. See maftools::getGeneSummary() for details.

• sample_summary: sample summary informations. See maftools::getSampleSummary() for details.

• sample_anno: sample clinical informations. See maftools::getClinicalData() for details.

• n_genes: Total of genes.

• n_samples: Total of samples.

• titv: A list of data.frames with Transitions and Transversions summary. See maftools::titv() for details.

See Also

Other fortify_matrix methods: fortify_matrix.GISTIC(), fortify_matrix.default()

Description

align_plots will try to align plot panels, and every elements of the plot, following functions romove these restrictions:

• free_align: if we want to compose plots without alignment of some panel axes (panel won't be aligned). we can wrap the plot with free_align.

• free_border: If we want to compose plots without alignment of the panel borders (but still align the panels themselves), we can wrap the plot with free_border.

• free_lab: If we want to compose plots without alignment of the axis title, we can wrap the plot with free_lab.

• free_space: Removing the ggplot element sizes when aligning.

• free_vp: Customize the viewport when aligning.

• free_guide: If we want to override the behaviour of the overall guides behaviour, we can wrap the plot with free_guide.

Usage

free_align(plot, axes = "tlbr")

free_border(plot, borders = "tlbr")

free_guide(plot, guides = "tlbr")

free_lab(plot, labs = "tlbr")

free_space(plot, spaces = "tlbr")

free_vp(plot, x = 0.5, y = 0.5, width = NA, height = NA, ...)

Arguments

Value

• free_align: A modified version of plot with a free_align class.

• free_border: A modified version of plot with a free_border class.

• free_guide: A modified version of plot with a free_guide class.

• free_lab: A modified version of plot with a free_lab class.

• free_space: A modified version of plot with a free_space class.

• free_vp: A modified version of plot with a free_vp class.

Examples

# directly copied from `patchwork`
# Sometimes you have a plot that defies good composition alginment, e.g. due
# to long axis labels
p1 <- ggplot(mtcars) +
    geom_bar(aes(y = factor(gear), fill = factor(gear))) +
    scale_y_discrete(
        "",
        labels = c(
            "3 gears are often enough",
            "But, you know, 4 is a nice number",
            "I would def go with 5 gears in a modern car"
        )
    )

# When combined with other plots it ends up looking bad
p2 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))

align_plots(p1, p2, ncol = 1L)

# We can fix this be using `free_align`
align_plots(free_align(p1), p2, ncol = 1L)

# If we still want the panels to be aligned to the right, we can choose to
# free only the left side
align_plots(free_align(p1, axes = "l"), p2, ncol = 1L)

# We could use `free_lab` to fix the layout in a different way
align_plots(p1, free_lab(p2), ncol = 1L)

# `free_border` is similar with `free_lab`, they have a distinction in terms
# of placement on either the top or bottom side of the panel. Specifically,
# the top side contains the `title` and `subtitle`, while the bottom side
# contains the `caption`. free_lab() does not attach these elements in the
# panel area.
p3 <- ggplot(mtcars) +
    geom_point(aes(hp, wt, colour = mpg)) +
    ggtitle("Plot 3")
p_axis_top <- ggplot(mtcars) +
    geom_point(aes(mpg, disp)) +
    ggtitle("Plot axis in top") +
    scale_x_continuous(position = "top")
align_plots(p_axis_top, free_lab(p3))
align_plots(p_axis_top, free_border(p3))

# Another issue is that long labels can occupy much spaces
align_plots(NULL, p1, p2, p2)

# This can be fixed with `free_space`
align_plots(NULL, free_space(p1, "l"), p2, p2)

Description

The free_gg() function allows you to incorporate a ggplot object into your layout. Unlike align_gg(), which aligns every axis value precisely, free_gg() focuses on layout integration without enforcing strict axis alignment. ggfree() is an alias for free_gg.

Usage

free_gg(..., data = waiver(), size = NULL, active = NULL)

## Default S3 method:
free_gg(mapping = aes(), ..., data = waiver(), size = NULL, active = NULL)

## S3 method for class 'ggplot'
free_gg(..., data = waiver(), size = NULL, active = NULL)

Arguments

Value

A ggalign_free_gg object.

Examples

ggheatmap(matrix(rnorm(56), nrow = 7)) +
    anno_top() +
    align_dendro() +
    ggfree(aes(wt, mpg), data = mtcars) +
    geom_point()

Description

Layer with customized draw function

Usage

geom_draw(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  lineend = "butt",
  linejoin = "mitre",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

Details

geom_draw depends on the new aesthetics draw, which should always be provided with scale_draw_manual(), in which, we can provide a list of functions that define how each cell's grob (graphical object) should be drawn. This aesthetic allows you to replace the default rendering of cells with custom behavior, making it possible to tailor the plot to specific requirements.

Aesthetics

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

• x

• y

• draw

• alpha

• colour

• fill

• group

• linetype

• linewidth

• shape

• size

• stroke

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

Examples

library(grid)
ggplot(data.frame(value = letters[seq_len(5)], y = seq_len(5))) +
    geom_draw(aes(x = 1, y = y, draw = value, fill = value)) +
    scale_draw_manual(values = list(
        a = function(x, y, width, height, fill) {
            rectGrob(x, y,
                width = width, height = height,
                gp = gpar(fill = fill),
                default.units = "native"
            )
        },
        b = function(x, y, width, height, fill) {
            rectGrob(x, y,
                width = width, height = height,
                gp = gpar(fill = fill),
                default.units = "native"
            )
        },
        c = function(x, y, width, height, fill) {
            rectGrob(x, y,
                width = width, height = height,
                gp = gpar(fill = fill),
                default.units = "native"
            )
        },
        d = function(x, y, width, height, shape) {
            gList(
                pointsGrob(x, y, pch = shape),
                # To ensure the rectangle color is shown in the legends, you
                # must explicitly provide a color argument and include it in
                # the `gpar()` of the graphical object
                rectGrob(x, y, width, height,
                    gp = gpar(col = "black", fill = NA)
                )
            )
        },
        e = function(xmin, xmax, ymin, ymax) {
            segmentsGrob(
                xmin, ymin,
                xmax, ymax,
                gp = gpar(lwd = 2)
            )
        }
    )) +
    scale_fill_brewer(palette = "Dark2") +
    theme_void()

Description

Pie charts

Usage

geom_pie(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  clockwise = TRUE,
  steps = 100,
  lineend = "butt",
  linejoin = "round",
  linemitre = 10,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

new aesthetics

• angle: the pie circle angle.

• angle0: the initial pie circle angle.

• radius: the circle radius.

Aesthetics

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

• x

• y

• angle

• alpha

• angle0

• colour

• fill

• group

• linetype

• linewidth

• radius

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

Examples

ggplot(data.frame(x = 1:10, y = 1:10, value = 1:10 / sum(1:10))) +
    geom_pie(aes(x, y, angle = value * 360))

Description

These geoms subdivide rectangles with shared borders into a grid. Both geoms achieve the same result but differ in how the rectangles are parameterized:

• geom_subrect(): Defines rectangles using their four corners (xmin, xmax, ymin, ymax).

• geom_subtile(): Defines rectangles using the center (x, y) and dimensions (width, height).

Usage

geom_subrect(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  byrow = TRUE,
  direction = NULL,
  lineend = "butt",
  linejoin = "mitre",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_subtile(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  byrow = TRUE,
  direction = NULL,
  lineend = "butt",
  linejoin = "mitre",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

Aesthetics

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

• xmin

• xmax

• ymin

• ymax

• alpha

• colour

• fill

• group

• linetype

• linewidth

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

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

• x

• y

• alpha

• colour

• fill

• group

• height

• linetype

• linewidth

• width

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

Examples

# arranges by row
ggplot(data.frame(value = letters[seq_len(5)])) +
    geom_subtile(aes(x = 1, y = 1, fill = value))

# arranges by column
ggplot(data.frame(value = letters[seq_len(9)])) +
    geom_subtile(aes(x = 1, y = 1, fill = value), byrow = FALSE)

# one-row
ggplot(data.frame(value = letters[seq_len(4)])) +
    geom_subtile(aes(x = 1, y = 1, fill = value), direction = "h")

# one-column
ggplot(data.frame(value = letters[seq_len(4)])) +
    geom_subtile(aes(x = 1, y = 1, fill = value), direction = "v")

Description

ggalign_attr provides access to supplementary information stored as attributes during the layout rendering process in quad_layout()/ggheatmap() or stack_layout() object. These attributes, commonly attached during data transformation by functions like fortify_matrix() or fortify_data_frame(), can include essential details such as filtered or supplementary data that inform downstream operations.

Usage

ggalign_attr(x, field = NULL)

Arguments

Details

Attributes attached to the data are particularly useful when input data is transformed in ways that restrict access to the complete dataset. For instance, fortify_matrix.MAF() might filter mutation data while adding attributes that retain essential context, such as the total number of observations, for detailed or aggregated analyses.

Value

The specified data from the attached attribute or NULL if it is unavailable.

Description

• ggalign_attr_set: Attaches supplementary data to the input, facilitating downstream use.

• ggalign_attr_get: Extracts previously attached supplementary data during the transformation process.

Usage

ggalign_attr_set(x, values)

ggalign_attr_get(x)

Arguments

Details

Attributes attached to the data are particularly useful when input data is transformed in ways that restrict access to the complete dataset. For instance, fortify_matrix.MAF() might filter mutation data while adding attributes that retain essential context, such as the total number of observations, for detailed or aggregated analyses.

See Also

ggalign_attr()

Description

Get the statistics from the layout

Usage

ggalign_stat(x, ...)

## S3 method for class 'QuadLayout'
ggalign_stat(x, position, ...)

## S3 method for class 'StackLayout'
ggalign_stat(x, what, ...)

Arguments

Value

The statistics

Description

Generate a plot grob.

Usage

ggalignGrob(x)

Arguments

Value

A grob() object.

Examples

ggalignGrob(ggplot())

Description

The ggoncoplot() function generates oncoPrint visualizations that display genetic alterations in a matrix format. This function is especially useful for visualizing complex genomic data, such as mutations, copy number variations, and other genomic alterations in cancer research.

Usage

ggoncoplot(
  data = NULL,
  mapping = aes(),
  ...,
  map_width = NULL,
  map_height = NULL,
  reorder_row = reorder_column,
  reorder_column = TRUE,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL
)

## Default S3 method:
ggoncoplot(
  data = NULL,
  mapping = aes(),
  ...,
  map_width = NULL,
  map_height = NULL,
  reorder_row = reorder_column,
  reorder_column = TRUE,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL
)

Arguments

Details

ggoncoplot() is a wrapper around the ggheatmap() function, designed to simplify the creation of OncoPrint-style visualizations. The function automatically processes the input character matrix by splitting the encoded alterations (delimited by ";", ":", ",", or "|") into individual genomic events and unnesting the columns for visualization.

Additionally, a predefined reordering function, adapted from https://gist.github.com/armish/564a65ab874a770e2c26, is included to enhance the organization of the alterations.

Value

A HeatmapLayout object.

Examples

# A simple example from `ComplexHeatmap`
mat <- read.table(textConnection(
    "s1,s2,s3
g1,snv;indel,snv,indel
g2,,snv;indel,snv
g3,snv,,indel;snv"
), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)

ggoncoplot(mat, map_width = c(snv = 0.5), map_height = c(indel = 0.9)) +
    # Note that guide legends from `geom_tile` and `geom_bar` are different.
    # Although they appear similar, the internal mechanisms won't collapse
    # the guide legends. Therefore, we remove the guide legends from
    # `geom_tile`.
    guides(fill = "none") +
    anno_top(size = 0.5) +
    ggalign() +
    geom_bar(aes(fill = value), data = function(x) {
        subset(x, !is.na(value))
    }) +
    anno_right(size = 0.5) +
    ggalign() +
    geom_bar(aes(fill = value), orientation = "y", data = function(x) {
        subset(x, !is.na(value))
    }) &
    scale_fill_brewer(palette = "Dark2", na.translate = FALSE)

Description

The ggwrap() function allows non-ggplot2 elements to be converted into a compliant representation for use with align_plots(). This is useful for adding any graphics that can be converted into a grob with the patch() method.

Usage

ggwrap(plot, ..., align = "panel", on_top = TRUE, clip = TRUE, vp = NULL)

Arguments

Value

A wrapped_plot object that can be directly placed into align_plots().

See Also

• patch.grob() / patch.gList()

• patch.ggplot()

• patch.patch_ggplot()

• patch.patchwork()

• patch.patch()

• patch.trellis()

• patch.formula() / patch.function()

• patch.recordedplot()

• patch.Heatmap()

• patch.HeatmapList()

• patch.HeatmapAnnotation()

• patch.pheatmap()

Examples

library(grid)
ggwrap(rectGrob(gp = gpar(fill = "goldenrod")), align = "full") +
    inset(rectGrob(gp = gpar(fill = "steelblue")), align = "panel") +
    inset(textGrob("Here are some text", gp = gpar(color = "black")),
        align = "panel"
    )
p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp)) +
    ggtitle("Plot 1")
align_plots(p1, ggwrap(
    ~ plot(mtcars$mpg, mtcars$disp),
    mar = c(0, 2, 0, 0), bg = NA
))

Description

Generate Tree Structures with Hierarchical Clustering

Usage

hclust2(
  matrix,
  distance = "euclidean",
  method = "complete",
  use_missing = "pairwise.complete.obs"
)

Arguments

Value

A hclust object.

See Also

• cor()

• dist()

• hclust()

Examples

hclust2(dist(USArrests), method = "ward.D")

Description

heatmap_layout is a specialized version of quad_alignb(), which simplifies the creation of heatmap plots by integrating essential elements for a standard heatmap layout, ensuring that the appropriate data mapping and visualization layers are automatically applied. ggheatmap is an alias for heatmap_layout.

Usage

heatmap_layout(
  data = NULL,
  mapping = aes(),
  ...,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL,
  set_context = deprecated(),
  order = deprecated(),
  name = deprecated(),
  guides = deprecated()
)

Arguments

Value

A HeatmapLayout object.

ggplot2 specification

The data input in ggheatmap will be converted into the long formated data frame when drawing. The default mapping will use aes(.data$.x, .data$.y), you can use mapping argument to control it. The data in the underlying ggplot object contains following columns:

• .xpanel and .ypanel: the column and row panel

• .x and .y: the x and y coordinates

• .row_names and .column_names: A factor of the row and column names of the original matrix (only applicable when names exist).

• .row_index and .column_index: the row and column index of the original matrix.

• value: the actual matrix value.

Examples

ggheatmap(1:10)
ggheatmap(letters)
ggheatmap(matrix(rnorm(81), nrow = 9L))

Description

Create a ggplot inset

Usage

inset(plot, ..., align = "panel", on_top = TRUE, clip = TRUE, vp = NULL)

Arguments

Value

A patch_inset object, which can be added in ggplot.

See Also

• patch.grob() / patch.gList()

• patch.ggplot()

• patch.patch_ggplot()

• patch.patchwork()

• patch.patch()

• patch.trellis()

• patch.formula() / patch.function()

• patch.recordedplot()

• patch.Heatmap()

• patch.HeatmapList()

• patch.HeatmapAnnotation()

• patch.pheatmap()

Examples

library(grid)
p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p1 + inset(p2, vp = viewport(0.6, 0.6,
    just = c(0, 0), width = 0.4, height = 0.4
))

Description

Reports whether x is layout object

Usage

is_layout(x)

is_quad_layout(x)

is_stack_layout(x)

is_heatmap_layout(x)

is_ggheatmap(x)

Arguments

Value

A single boolean value.

Examples

is_layout(ggheatmap(1:10))

# for quad_layout()
is_quad_layout(quad_alignb(1:10))
is_quad_layout(quad_alignh(1:10))
is_quad_layout(quad_alignv(1:10))
is_quad_layout(quad_free(mtcars))

# for stack_layout()
is_stack_layout(stack_align(1:10))
is_stack_layout(stack_free(1:10))

# for heatmap_layout()
is_heatmap_layout(ggheatmap(1:10))
is_ggheatmap(ggheatmap(1:10))

Description

This function allows you to change the order in which layers are added to a ggplot.

Usage

layer_order(layer, order = 0)

Arguments

Value

A layer_order object.

Examples

ggplot(faithfuld, aes(waiting, eruptions)) +
    geom_raster(aes(fill = density)) +
    geom_point(color = "red", size = 1)
ggplot(faithfuld, aes(waiting, eruptions)) +
    geom_raster(aes(fill = density)) +
    layer_order(geom_point(color = "red", size = 1))

Description

• modify the theme of the layout

Usage

layout_annotation(theme = waiver(), ...)

Arguments

Details

• guides, patch.title, panel.border, and background will always be added even for the nested alignpatches object.

• title, subtitle, caption, and margins will be added for the top-level alignpatches object only.

Examples

p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p3 <- ggplot(mtcars) +
    geom_bar(aes(gear)) +
    facet_wrap(~cyl)
align_plots(
    p1 + theme(plot.background = element_blank()),
    p2 + theme(plot.background = element_blank()),
    p3 + theme(plot.background = element_blank())
) +
    layout_annotation(
        theme = theme(plot.background = element_rect(fill = "red"))
    )

Description

To control how different plots are laid out, you need to add a layout design specification. If you are nesting grids, the layout is scoped to the current nesting level.

Usage

layout_design(
  ncol = waiver(),
  nrow = waiver(),
  byrow = waiver(),
  widths = waiver(),
  heights = waiver(),
  design = waiver(),
  guides = NA
)

Arguments

Value

A layout_design object.

Examples

p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p3 <- ggplot(mtcars) +
    geom_bar(aes(gear)) +
    facet_wrap(~cyl)
align_plots(p1, p2, p3) +
    layout_design(nrow = 1L)
align_plots(p1, p2, p3) +
    layout_design(ncol = 1L)

Description

Annotate the whole layout

Usage

layout_title(title = waiver(), subtitle = waiver(), caption = waiver())

Arguments

Value

A layout_title object.

Examples

p1 <- ggplot(mtcars) +
    geom_point(aes(mpg, disp))
p2 <- ggplot(mtcars) +
    geom_boxplot(aes(gear, disp, group = gear))
p3 <- ggplot(mtcars) +
    geom_bar(aes(gear)) +
    facet_wrap(~cyl)
align_plots(p1, p2, p3) +
    layout_title(title = "I'm title")

Description

• +: Adds elements to the active plot in the active layout.

• &: Applies elements to all plots in the layout.

• -: Adds elements to multiple plots in the layout.

Usage

## S4 method for signature 'QuadLayout,ANY'
Ops(e1, e2)

## S4 method for signature 'StackLayout,ANY'
Ops(e1, e2)

Arguments

Details

The + operator is straightforward and should be used as needed.

In order to reduce code repetition ggalign provides two operators for adding ggplot elements (geoms, themes, facets, etc.) to multiple/all plots in quad_layout()/ggheatmap() or stack_layout() object: - and &. See vignette("operator") for details.

Value

A modified Layout object.

Examples

set.seed(123)
small_mat <- matrix(rnorm(56), nrow = 7)
ggheatmap(small_mat) +
    anno_top() +
    ggalign() +
    geom_point(aes(y = value))

# `&` operator apply it to all plots
ggheatmap(small_mat) +
    anno_top() +
    align_dendro() &
    theme(panel.border = element_rect(
        colour = "red", fill = NA, linewidth = unit(2, "mm")
    ))

# If the active layout is the annotation stack, the `-` operator will only
# add the elements to all plots in the active annotation stack:
ggheatmap(small_mat) +
    anno_left(size = 0.2) +
    align_dendro(aes(color = branch), k = 3L) +
    align_dendro(aes(color = branch), k = 3L) -
    # Modify the the color scales of all plots in the left annotation
    scale_color_brewer(palette = "Dark2")

# If the active layout is the `ggstack()`/`stack_layout()` itself, `-`
# applies the elements to all plots in the layout except the nested
# `ggheatmap()`/`quad_layout()`.
stack_alignv(small_mat) +
    align_dendro() +
    ggtitle("I'm from the parent stack") +
    ggheatmap() +
    # remove any active context
    stack_active() +
    align_dendro() +
    ggtitle("I'm from the parent stack") -
    # Modify the the color scales of all plots in the stack layout except the
    # heatmap layout
    scale_color_brewer(palette = "Dark2") -
    # set the background of all plots in the stack layout except the heatmap
    # layout
    theme(plot.background = element_rect(fill = "red"))

Description

order2 returns a permutation which rearranges its first argument into ascending order.

Usage

order2(x)

## S3 method for class 'hclust'
order2(x)

## S3 method for class 'dendrogram'
order2(x)

## S3 method for class 'ser_permutation_vector'
order2(x)

## S3 method for class 'ser_permutation'
order2(x)

Arguments

Value

An integer vector unless any of the inputs has 2^31 or more elements, when it is a double vector.

Examples

order2(hclust2(matrix(rnorm(100L), nrow = 10L)))

Description

This function extends ggplot2's title functionality, allowing you to add titles to each border of the plot: top, left, bottom, and right.

Usage

patch_titles(
  top = waiver(),
  left = waiver(),
  bottom = waiver(),
  right = waiver()
)

Arguments

Details

You can also use labs() to specify the titles (use arguments "top", "left", "bottom", and "right") for the top, left, bottom, and right borders of the plot.

The appearance and alignment of these patch titles can be customized using theme():

• plot.patch_title/⁠plot.patch_title.*⁠: Controls the text appearance of patch titles. By default, plot.patch_title inherit from plot.title, and settings for each border will inherit from plot.patch_title, with the exception of the angle property, which is not inherited.

• plot.patch_title.position/⁠plot.patch_title.position.*⁠: Determines the alignment of the patch titles. By default, plot.patch_title.position inherit from plot.title.position, and settings for each border will inherit from plot.patch_title. The value "panel" aligns the patch titles with the plot panels. Setting this to "plot" aligns the patch title with the entire plot (excluding margins and plot tags).

Value

A labels object to be added to ggplot.

Examples

ggplot(mtcars) +
    geom_point(aes(mpg, disp)) +
    patch_titles(
        top = "I'm top patch title",
        left = "I'm left patch title",
        bottom = "I'm bottom patch title",
        right = "I'm right patch title"
    )

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'alignpatches'
patch(x, ...)

Arguments

Value

A grob object.

See Also

alignpatches

Other patch methods: patch.Heatmap(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'formula'
patch(x, ..., device = NULL, name = NULL)

## S3 method for class ''function''
patch(x, ..., device = NULL, name = NULL)

Arguments

Value

A grob object.

See Also

plot()

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'ggplot'
patch(x, ...)

Arguments

Value

A grob object.

See Also

ggplot

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'grob'
patch(x, ...)

## S3 method for class 'gList'
patch(x, ...)

Arguments

Value

A grob object.

See Also

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'Heatmap'
patch(x, ..., device = NULL)

## S3 method for class 'HeatmapList'
patch(x, ..., device = NULL)

## S3 method for class 'HeatmapAnnotation'
patch(x, ..., device = NULL)

Arguments

Value

A grob object.

See Also

• Heatmap()

• HeatmapAnnotation()

Other patch methods: patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'patch'
patch(x, ...)

Arguments

Value

A grob object.

See Also

patch

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'patch_ggplot'
patch(x, ...)

Arguments

Value

A grob object.

See Also

• patch_titles()

• inset()

• ggwrap()

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patchwork(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'patchwork'
patch(x, ...)

Arguments

Value

A grob object.

See Also

patchwork

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.pheatmap(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'pheatmap'
patch(x, ...)

Arguments

Value

A grob object.

See Also

pheatmap()

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.recordedplot(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'recordedplot'
patch(x, ..., device = NULL)

Arguments

Value

A grob object.

See Also

recordPlot()

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.trellis()

Description

The patch() function is used by ggwrap() and inset() to convert objects into a grob.

Usage

## S3 method for class 'trellis'
patch(x, ..., device = NULL)

Arguments

Value

A grob object.

See Also

trellis

Other patch methods: patch.Heatmap(), patch.alignpatches(), patch.formula(), patch.ggplot(), patch.grob(), patch.patch(), patch.patch_ggplot(), patch.patchwork(), patch.pheatmap(), patch.recordedplot()

Description

The plot_align() function defines the align Specifications for plots.

Usage

plot_align(guides = NA, free_spaces = NA, free_labs = NA)

Arguments

Value

A plot_align object.

Examples

set.seed(123)
mat <- matrix(rnorm(72), nrow = 8)
# used in the layout, define the default action for all plots in the layout
ggheatmap(mat) -
    plot_align(guides = NULL) +
    anno_right() +
    align_dendro(aes(color = branch), k = 3)

# You can also add it for a single plot
ggheatmap(mat) -
    # for all plots in the layout, we default won't collect any guide legends
    plot_align(guides = NULL) +
    # for the heatmap body, we collect guide legends in the right
    # note, the guide legends will be collected to the right side of the
    # layout which will overlap the legends in the right annotation
    plot_align(guides = "r") +
    anno_right() +
    align_dendro(aes(color = branch), k = 3)

# to avoid overlapping, we can also collect the guide legends in the
# right annotation
ggheatmap(mat) -
    plot_align(guides = NULL) +
    plot_align(guides = "r") +
    anno_right() +
    align_dendro(aes(color = branch), k = 3) +
    plot_align(guides = "r")

Description

Transforms the plot data. Many functions in this package require a specific data format to align observations, plot_data() helps reformat data frames as needed.

Usage

plot_data(data, inherit = FALSE)

Arguments

Details

Defaults will attempt to inherit from the parent layout if the actual data is inherited from the parent layout, with one exception: align_dendro(), which will not inherit the plot_data by default.

Description

plot_theme() serves as the default theme and will always be overridden by any theme() settings applied directly to the plot. The default theme (plot_theme()) is applied first, followed by any specific theme() settings, even if theme() is added before plot_theme().

Usage

plot_theme(
  ...,
  line,
  rect,
  text,
  title,
  aspect.ratio,
  axis.title,
  axis.title.x,
  axis.title.x.top,
  axis.title.x.bottom,
  axis.title.y,
  axis.title.y.left,
  axis.title.y.right,
  axis.text,
  axis.text.x,
  axis.text.x.top,
  axis.text.x.bottom,
  axis.text.y,
  axis.text.y.left,
  axis.text.y.right,
  axis.text.theta,
  axis.text.r,
  axis.ticks,
  axis.ticks.x,
  axis.ticks.x.top,
  axis.ticks.x.bottom,
  axis.ticks.y,
  axis.ticks.y.left,
  axis.ticks.y.right,
  axis.ticks.theta,
  axis.ticks.r,
  axis.minor.ticks.x.top,
  axis.minor.ticks.x.bottom,
  axis.minor.ticks.y.left,
  axis.minor.ticks.y.right,
  axis.minor.ticks.theta,
  axis.minor.ticks.r,
  axis.ticks.length,
  axis.ticks.length.x,
  axis.ticks.length.x.top,
  axis.ticks.length.x.bottom,
  axis.ticks.length.y,
  axis.ticks.length.y.left,
  axis.ticks.length.y.right,
  axis.ticks.length.theta,
  axis.ticks.length.r,
  axis.minor.ticks.length,
  axis.minor.ticks.length.x,
  axis.minor.ticks.length.x.top,
  axis.minor.ticks.length.x.bottom,
  axis.minor.ticks.length.y,
  axis.minor.ticks.length.y.left,
  axis.minor.ticks.length.y.right,
  axis.minor.ticks.length.theta,
  axis.minor.ticks.length.r,
  axis.line,
  axis.line.x,
  axis.line.x.top,
  axis.line.x.bottom,
  axis.line.y,
  axis.line.y.left,
  axis.line.y.right,
  axis.line.theta,
  axis.line.r,
  legend.background,
  legend.margin,
  legend.spacing,
  legend.spacing.x,
  legend.spacing.y,
  legend.key,
  legend.key.size,
  legend.key.height,
  legend.key.width,
  legend.key.spacing,
  legend.key.spacing.x,
  legend.key.spacing.y,
  legend.frame,
  legend.ticks,
  legend.ticks.length,
  legend.axis.line,
  legend.text,
  legend.text.position,
  legend.title,
  legend.title.position,
  legend.position,
  legend.position.inside,
  legend.direction,
  legend.byrow,
  legend.justification,
  legend.justification.top,
  legend.justification.bottom,
  legend.justification.left,
  legend.justification.right,
  legend.justification.inside,
  legend.location,
  legend.box,
  legend.box.just,
  legend.box.margin,
  legend.box.background,
  legend.box.spacing,
  panel.background,
  panel.border,
  panel.spacing,
  panel.spacing.x,
  panel.spacing.y,
  panel.grid,
  panel.grid.major,
  panel.grid.minor,
  panel.grid.major.x,
  panel.grid.major.y,
  panel.grid.minor.x,
  panel.grid.minor.y,
  panel.ontop,
  plot.background,
  plot.title,
  plot.title.position,
  plot.subtitle,
  plot.caption,
  plot.caption.position,
  plot.tag,
  plot.tag.position,
  plot.tag.location,
  plot.margin,
  strip.background,
  strip.background.x,
  strip.background.y,
  strip.clip,
  strip.placement,
  strip.text,
  strip.text.x,
  strip.text.x.bottom,
  strip.text.x.top,
  strip.text.y,
  strip.text.y.left,
  strip.text.y.right,
  strip.switch.pad.grid,
  strip.switch.pad.wrap,
  complete = FALSE,
  validate = TRUE
)

Arguments