A function used to draw the links. The function must return a grob() object. If the function does not return a valid grob, no drawing will occur. The input data for the function contains a list, where each item is a list of two data frames: one for the left hand coordinates ("hand1") and one for the right hand observations coordinates ("hand2").

<dyn-dots> A list of formulas, where each side of the formula should be an integer or character index of the original data, or a range_link() object defining the linked observations. Use NULL to indicate no link on that side. You can also combine these by wrapping them into a single list(). If only the left-hand side of the formula exists, you can input it directly. For integer indices, wrap them with I() to use the ordering from the layout. You can also use waiver() to inherit values from the other group.

A function used to draw the links. The function must return a grob() object. If the function does not return a valid grob, nothing will be drawn. The input data for the function contains a list, where each item is a list of two data frames: one for the panel side coordinates ("panel") and one for the marked observations coordinates ("link").

<dyn-dots> A list of formulas, where each side of the formula should be an integer or character index of the original data, or a range_link() object defining the linked observations. Use NULL to indicate no link on that side. You can also combine these by wrapping them into a single list(). If only the left-hand side of the formula exists, you can input it directly. For integer indices, wrap them with I() to use the ordering from the layout. You can also use waiver() to inherit values from the other group.

A Layout object

A string of property name in Layout object.

<dyn-dots> A list of Scheme object.

An integer specifying the order of the plot area within the layout.

A logical (TRUE/FALSE) indicating whether to set the active context to the current plot when added to a layout. If TRUE, any subsequent ggplot elements will be applied to this plot.

A string specifying the plot's name, useful for switching active contexts through the what argument in functions like quad_anno()/stack_switch().

An CraftAlign object.

The following options can be used:

• NULL: No data is set.

• waiver(): Inherits the data from the layout matrix.

• A function (including purrr-like lambda syntax): Applied to the layout matrix to transform the data before use. To transform the final plot data, please use scheme_data().

• A matrix, data.frame, or atomic vector.

Additional fields passed to the align object.

A ggplot object.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

Options for schemes:

• NULL: Used when align do not add a plot.

• waiver(): Try to infer schemes based on data.

A active() object that defines the context settings when added to a layout.

Please add theme() directly to the ggplot instead.

The call used to construct the align object, for reporting messages.

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

<dyn-dots> Additional arguments passed to geom_segment().

A string of distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Correlation coefficient can be also used, including "pearson", "spearman" or "kendall". In this way, 1 - cor will be used as the distance. In addition, you can also provide a dist object directly or a function return a dist object. Use NULL, if you don't want to calculate the distance.

A string of the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). You can also provide a function which accepts the calculated distance (or the input matrix if distance is NULL) and returns a hclust object. Alternative, you can supply an object which can be coerced to hclust.

An optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs". Only used when distance is a correlation coefficient string.

A single boolean value indicating whether to reorder the dendrogram based on the means. Alternatively, you can provide a custom function that accepts an hclust object and the data used to generate the tree, returning either an hclust or dendrogram object. Default is FALSE.

A single boolean value, indicates whether we should merge multiple dendrograms, only used when previous groups have been established. Default: FALSE.

A single boolean value, indicates whether we should do Hierarchical Clustering between groups, only used when previous groups have been established. Default: FALSE.

An integer scalar indicates the desired number of groups.

A numeric scalar indicates heights where the tree should be cut.

A function used to cut the hclust tree. It should accept four arguments: the hclust tree object, distance (only applicable when method is a string or a function for performing hierarchical clustering), k (the number of clusters), and h (the height at which to cut the tree). By default, cutree() is used.

A boolean value indicates whether plot the dendrogram tree.

A boolean value indicates whether plot the cut height.

A boolean value. if TRUE, nodes are plotted centered with respect to all leaves/tips in the branch. Otherwise (default), plot them in the middle of the direct child nodes.

A string indicates the plot type, "rectangle" or "triangle".

A length one string or numeric indicates the root branch.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A matrix-like object. By default, it inherits from the layout matrix.

A active() object that defines the context settings when added to a layout.

Please add theme() directly to the ggplot instead.

A character define the groups of the observations.

A active() object that defines the context settings when added to a layout.

A string of distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Correlation coefficient can be also used, including "pearson", "spearman" or "kendall". In this way, 1 - cor will be used as the distance. In addition, you can also provide a dist object directly or a function return a dist object. Use NULL, if you don't want to calculate the distance.

A string of the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). You can also provide a function which accepts the calculated distance (or the input matrix if distance is NULL) and returns a hclust object. Alternative, you can supply an object which can be coerced to hclust.

An optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs". Only used when distance is a correlation coefficient string.

A single boolean value indicating whether to reorder the dendrogram based on the means. Alternatively, you can provide a custom function that accepts an hclust object and the data used to generate the tree, returning either an hclust or dendrogram object. Default is FALSE.

A single boolean value, indicates whether we should do Hierarchical Clustering between groups, only used when previous groups have been established. Default: FALSE.

An integer scalar indicates the desired number of groups.

A numeric scalar indicates heights where the tree should be cut.

A function used to cut the hclust tree. It should accept four arguments: the hclust tree object, distance (only applicable when method is a string or a function for performing hierarchical clustering), k (the number of clusters), and h (the height at which to cut the tree). By default, cutree() is used.

A matrix-like object. By default, it inherits from the layout matrix.

A active() object that defines the context settings when added to a layout.

Arguments passed on to stats::kmeans

iter.max

the maximum number of iterations allowed.

nstart

if centers is a number, how many random sets should be chosen?

algorithm

character: may be abbreviated. Note that "Lloyd" and "Forgy" are alternative names for one algorithm.

trace

logical or integer number, currently only used in the default method ("Hartigan-Wong"): if positive (or true), tracing information on the progress of the algorithm is produced. Higher values may produce more tracing information.

A numeric matrix to be used by k-means. By default, it will inherit from the layout matrix.

A active() object that defines the context settings when added to a layout.

A summary function which accepts a data and returns the weights for each observations. Alternatively, you can provide an ordering index as either an integer or a character. Since characters have been designated as character indices, if you wish to specify a function name as a string, you must enclose it with I().

<dyn-dots> Additional arguments passed to function provided in weights argument.

A boolean value. Should the sort order be in reverse?

A boolean value indicates whether the order should be strict. If previous groups has been established, and strict is FALSE, this will reorder the observations in each group.

A matrix, ⁠data frame⁠, or atomic vector used as the input for the weights function. Alternatively, you can specify a function (including purrr-like lambda syntax) that will be applied to the layout matrix, transforming it as necessary for weight calculations. By default, it will inherit from the layout matrix.

A active() object that defines the context settings when added to a layout.

A statistical function which accepts a data and returns the statistic, which we'll call order2() to extract the ordering information.

<dyn-dots> Additional arguments passed to function provided in stat argument.

A boolean value. Should the sort order be in reverse?

A boolean value indicates whether the order should be strict. If previous groups has been established, and strict is FALSE, this will reorder the observations in each group.

A matrix, ⁠data frame⁠, or atomic vector used as the input for the stat function. Alternatively, you can specify a function (including purrr-like lambda syntax) that will be applied to the layout matrix, transforming it as necessary for statistic calculations. By default, it will inherit from the layout matrix.

A active() object that defines the context settings when added to a layout.

A phylo object.

<dyn-dots> Additional arguments passed to geom_segment().

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

A logical scalar indicating whether to split the phylogenetic tree into separate subtrees when multiple panel groups are present.

A single string of "left" or "right", indicating whether to ladderize the tree. Ladderizing arranges the tree so that the smallest clade is positioned on the "right" or the "left". By default, NULL means the tree will not be ladderized.

A string indicates the plot type, "rectangle" or "triangle".

A boolean value. if TRUE, nodes are plotted centered with respect to all leaves/tips in the branch. Otherwise (default), plot them in the middle of the direct child nodes.

A single string, one of "phylogram" or "cladogram", indicating the type of tree.

• phylogram: Represents a phylogenetic tree where branch lengths indicate evolutionary distance or time.

• cladogram: Represents a tree where branch lengths are not used, or the branches do not reflect evolutionary time.

Usually, you don't need to modify this.

A length one string or numeric indicates the root branch.

A active() object that defines the context settings when added to a layout.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

Please add theme() directly to the ggplot instead.

<dyn-dots> A list of plots, ususally the ggplot object. Use NULL to indicate an empty spacer.

The dimensions of the grid to create - if both are NULL it will use the same logic as facet_wrap() to set the dimensions

If FALSE the plots will be filled in in column-major order.

The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid. The special value of NA will behave as ⁠1null⁠ unit unless a fixed aspect plot is inserted in which case it will allow the dimension to expand or contract to match the aspect ratio of the content.

Specification of the location of areas in the layout. Can either be specified as a text string or by concatenating calls to area() together.

A string with one or more of "t", "l", "b", "r", and "i" indicating which side of guide legends should be collected. Defaults to waiver(), which inherits from the parent layout. If there is no parent layout, or if NULL is provided, no guides will be collected.

A theme() object used to customize various elements of the layout. By default, the theme will inherit from the parent layout.

An alias for area, retained for backward compatibility.

A plot object to be prepared for alignment.

The top and bottom bounds of the area in the grid

The left and right bounds of the area int the grid

The input data, which can be:

• A character string ("hg19" or "hg38") to load a predefined cytoband reference.

• A data.frame with at least three columns: chromosome, start, and end positions.

• A genomic object convertible via fortify_data_frame().

Additional arguments passed to specific methods or fortify_data_frame().

A coord_circle()/coord_radial() object that defines the global parameters for coordinate across all plots in the layout. The parameters start, end, direction, and expand will be inherited and applied uniformly to all plots within the layout. The parameters theta and r.axis.inside will always be ignored and will be set to "x" and TRUE, respectively, for all plots.

A single string of "inward" or "outward", indicating the direction in which the plot is added.

• outward: The plot is added from the inner to the outer.

• inward: The plot is added from the outer to the inner.

The size of spacing between different panel. A numeric of the radians or a rel() object.

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

Default dataset to use for the layout. If not specified, it must be supplied in each plot added to the layout:

• If limits is not provided, fortify_matrix() will be used to get a matrix.

• If limits is specified, fortify_data_frame() will be used to get a data frame.

Additional arguments passed to fortify_data_frame() or fortify_matrix().

A coord_circle()/coord_radial() object that defines the global parameters for coordinate across all plots in the layout. The parameters start, end, direction, and expand will be inherited and applied uniformly to all plots within the layout. The parameters theta and r.axis.inside will always be ignored and will be set to "x" and TRUE, respectively, for all plots.

A single string of "inward" or "outward", indicating the direction in which the plot is added.

• outward: The plot is added from the inner to the outer.

• inward: The plot is added from the outer to the inner.

The size of spacing between different panel. A numeric of the radians or a rel() object.

A continuous_limits() object specifying the left/lower limit and the right/upper limit of the scale. Used to align the continuous axis.

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

Please use sector_spacing instead.

A coord_circle()/coord_radial() object that defines the global parameters for coordinate across all plots in the layout. The parameters start, end, direction, and expand will be inherited and applied uniformly to all plots within the layout. The parameters theta and r.axis.inside will always be ignored and will be set to "x" and TRUE, respectively, for all plots.

A single string of "inward" or "outward", indicating the direction in which the plot is added.

• outward: The plot is added from the inner to the outer.

• inward: The plot is added from the outer to the inner.

What should get activated for the circle_layout()? A single number or string of the plot elements in the layout. If NULL, will remove any active context.

These dots are for future extensions and must be empty.

A list of two numeric values, specifying the left/lower limit and the right/upper limit of the scale.

variable to map angle to (x or y)

Offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction.

Position from 12 o'clock in radians where plot ends, to allow for partial polar coordinates. The default, NULL, is set to start + 2 * pi.

Limits for the theta and r axes.

If TRUE, the default, adds a small expansion factor to the limits to prevent overlap between data and axes. If FALSE, limits are taken directly from the scale.

1, clockwise; -1, anticlockwise

Should drawing be clipped to the extent of the plot panel? A setting of "on" (the default) means yes, and a setting of "off" means no. For details, please see coord_cartesian().

One of the following:

• NULL (default) places the axis next to the panel if start and end arguments form a full circle and inside the panel otherwise.

• TRUE to place the radius axis inside the panel.

• FALSE to place the radius axis next to the panel.

• A numeric value, setting a theta axis value at which the axis should be placed inside the panel. Can be given as a length 2 vector to control primary and secondary axis placement separately.

If TRUE, transforms the angle aesthetic in data in accordance with the computed theta position. If FALSE (default), no such transformation is performed. Can be useful to rotate text geoms in alignment with the coordinates.

A numeric in ⁠[0, 1)⁠ indicates the inner radius.

A numeric in ⁠(0, 1]⁠ indicates the outer radius. coord_radial() by default uses 0.8.

A link_draw() object that defines how to draw the links, such as link_line().

The dataset to use for the layout. By default, fortify_matrix() will convert the data to a matrix. This argument allows you to change the layout data. If not specified, the original data will be used.

<dyn-dots> Additional arguments passed to fortify_matrix().

A boolean value indicating whether to draw the link on top of the plot panel (TRUE) or below (FALSE).

A single numeric value that indicates the size of a single observation, ranging from ⁠(0, 1]⁠.

A boolean value indicating whether to inherit the ordering index. If TRUE, will match the layout ordering index with the data names.

A boolean value indicating whether to inherit the panel group. If TRUE, will match the layout panel with the data names.

A boolean value indicating whether to inherit the number of observations (nobs). If TRUE, the data input must be compatible with the layout data.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

A mark_draw() object to define how to draw the links. Like mark_line(), mark_tetragon(). Note the names of the pair links will be used to define the panel names so must be unique.

The dataset to use for the layout. By default, fortify_matrix() will convert the data to a matrix. This argument allows you to change the layout data. If not specified, the original data will be used.

<dyn-dots> Additional arguments passed to fortify_matrix().

A single numeric value that indicates the size of a single observation, ranging from ⁠(0, 1]⁠.

A boolean value indicating whether to inherit the ordering index. If TRUE, will match the layout ordering index with the data names.

A boolean value indicating whether to inherit the panel group. If TRUE, will match the layout panel with the data names.

A boolean value indicating whether to inherit the number of observations (nobs). If TRUE, the data input must be compatible with the layout data.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

The dataset to use for the layout. By default, fortify_matrix() will convert the data to a matrix. This argument allows you to change the layout data. If not specified, the original data will be used.

<dyn-dots> Additional arguments passed to fortify_matrix().

A boolean value indicating whether to inherit the ordering index. If TRUE, will match the layout ordering index with the data names.

A boolean value indicating whether to inherit the panel group. If TRUE, will match the layout panel with the data names.

A boolean value indicating whether to inherit the number of observations (nobs). If TRUE, the data input must be compatible with the layout data.

A single row data frame containing the scaled aesthetics to display in this key

A list of additional parameters supplied to the geom.

Width and height of key in mm.

An element object.

Additional arguments passed on to fn.

The function to be applied to the vectorized fields of the element object.

Non-negative integer. The desired length of the output vector. Other inputs will be coerced to a double vector and the first element taken. Ignored if NA or invalid.

Desired output size.

For vec_rep(), a single integer for the number of times to repeat the entire vector.

For vec_rep_each(), an integer vector of the number of times to repeat each element of x. times will be recycled to the size of x.

An integer, character or logical vector specifying the locations or names of the observations to get/set. Specify TRUE to index all elements (as in x[]), or NULL, FALSE or integer() to index none (as in x[NULL]).

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, can also be a formula or character vector. Use either a one sided formula, ~a + b, or a character vector, c("a", "b").

The size of spacing between different panel. A numeric of the radians or a rel() object.

If TRUE, the default, all factor levels not used in the data will automatically be dropped. If FALSE, all factor levels will be shown, regardless of whether or not they appear in the data.

Please add the coordinate system directly to the ggplot instead.

Please use sector_spacing instead.

An object to be converted to a data frame.

Arguments passed to methods.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

An object to be converted to a data frame.

Arguments passed to methods.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

An object to be converted to a data frame.

These dots are for future extensions and must be empty.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

An object to be converted to a data frame.

Additional arguments passed to fortify().

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A hclust or a dendrogram object.

Additional arguments passed to dendrogram method.

A string of "left" or "right". if we draw from right to left, the left will override the right, so we take the "left" as the priority. If we draw from left to right, the right will override the left, so we take the "right" as priority. This is used by align_dendro() to provide support of facet operation in ggplot2.

A boolean value. if TRUE, nodes are plotted centered with respect to all leaves/tips in the branch. Otherwise (default), plot them in the middle of the direct child nodes.

A string indicates the plot type, "rectangle" or "triangle".

The x-coordinates of the leaf node. Must be the same length of the number of observations in data.

Branches of the leaf node. Must be the same length of the number of observations in data. Usually come from cutree.

A single boolean value, indicates whether reorder the provided leaf_braches based on the actual index.

A single numeric value indicates the gap between different branches.

A length one string or numeric indicates the root branch.

A single logical value indicating whether horizontal lines should be doubled when segments span multiple branches. If TRUE, the horizontal lines will be repeated for each branch that the segment spans. If FALSE, only one horizontal line will be drawn. This is used by align_dendro() to provide support of facet operation in ggplot2.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A matrix-like object.

A logical value indicating whether to restore factor levels using those stored in ggalign_lvls(), or a character vector specifying custom levels for the value column. If levels are provided or restored, the value column will be returned as a factor.

These dots are for future extensions and must be empty.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A hclust or a dendrogram object.

These dots are for future extensions and must be empty.

A string of "left" or "right". if we draw from right to left, the left will override the right, so we take the "left" as the priority. If we draw from left to right, the right will override the left, so we take the "right" as priority. This is used by align_dendro() to provide support of facet operation in ggplot2.

A boolean value. if TRUE, nodes are plotted centered with respect to all leaves/tips in the branch. Otherwise (default), plot them in the middle of the direct child nodes.

A string indicates the plot type, "rectangle" or "triangle".

A single string, one of "phylogram" or "cladogram", indicating the type of tree.

• phylogram: Represents a phylogenetic tree where branch lengths indicate evolutionary distance or time.

• cladogram: Represents a tree where branch lengths are not used, or the branches do not reflect evolutionary time.

Usually, you don't need to modify this.

The x-coordinates of the tip. Must be the same length of the number of tips in tree.

Clades of the tips. Must be the same length of the number of tips in data.

A single boolean value, indicates whether reorder the provided tip_clades based on the actual ordering index.

A single numeric value indicates the gap between different clades.

A length one string or numeric indicates the root branch.

A single logical value indicating whether horizontal lines should be doubled when segments span multiple branches. If TRUE, the horizontal lines will be repeated for each branch that the segment spans. If FALSE, only one horizontal line will be drawn. This is used by align_dendro() to provide support of facet operation in ggplot2.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

An object to be converted into a matrix.

Additional arguments passed to methods.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A GISTIC object.

These dots are for future extensions and must be empty.

A single number indicates how many top bands to be drawn.

An atomic character defines the bands to draw.

An atomic character defines the bands to be ignored.

A data frame of sample clinical features to be added.

A single boolean value indicating whether to drop samples without any genomic alterations.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A MAF object.

These dots are for future extensions and must be empty.

An atomic character defines the genes to draw.

A single number indicates how many top genes to be drawn.

A single boolean value indicats whether to drop genes without any genomic alterations.

A single boolean value indicats whether to drop samples without any genomic alterations.

A single boolean value indicating whether to collapse multiple alterations in the same sample and gene into a single value "Multi_Hit". Alternatively, you can provide a single string indicates the collapsed values.

A single boolean value indicates whether to include synonymous variants when Classifies SNPs into transitions and transversions.

A string, either "error" or "remove", specifying the action for handling missing genes.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A string of "smgbp" or "sigpw", or a named list of genes to define the pathways.

A single boolean value indicats whether to drop pathways without any genomic alterations.

An object to be converted into a matrix.

These dots are for future extensions and must be empty.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A list of sets.

A string of "distinct", "intersect", or "union" indicates the mode to define the set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode for details.

These dots are for future extensions and must be empty.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A matrix object.

These dots are for future extensions and must be empty.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A matrix where each row represents an genes, and each column represents samples. The values in the matrix indicate whether the element is part of the set.

These dots are for future extensions and must be empty.

An atomic character defines the genes to draw.

A single number indicates how many top genes to be drawn.

A single boolean value indicats whether to drop genes without any genomic alterations.

A single boolean value indicats whether to drop samples without any genomic alterations.

A string, either "error" or "remove", specifying the action for handling missing genes.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A matrix where each row represents an element, and each column defines a set. The values in the matrix indicate whether the element is part of the set. Any non-missing value signifies that the element exists in the set.

Arguments passed on to fortify_matrix.list_upset

mode

A string of "distinct", "intersect", or "union" indicates the mode to define the set intersections. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/upset-plot.html#upset-mode for details.

The argument name for data. Developers can use it to improve messages. Not used by the user.

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

A ggplot or alignpatches object.

Which axes shouldn't be aligned? A string containing one or more of "t", "l", "b", and "r".

Which border shouldn't be aligned? A string containing one or more of "t", "l", "b", and "r".

A string containing one or more of "t", "l", "b", "r", and "i" indicates which side of guide legends should be collected for the plot. If NULL, no guide legends will be collected.

Which axis labs to be free? A string containing one or more of "t", "l", "b", and "r".

Which border spaces should be removed? A string containing one or more of "t", "l", "b", and "r".

A numeric vector or unit object specifying x-location.

A numeric vector or unit object specifying y-location.

A numeric vector or unit object specifying width.

A numeric vector or unit object specifying height.

Arguments passed on to grid::viewport

default.units

A string indicating the default units to use if x, y, width, or height are only given as numeric vectors.

just

A string or numeric vector specifying the justification of the viewport relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: "left", "right", "centre", "center", "bottom", and "top". For numeric values, 0 means left alignment and 1 means right alignment.

gp

An object of class "gpar", typically the output from a call to the function gpar. This is basically a list of graphical parameter settings.

clip

One of "on", "inherit", or "off", indicating whether to clip to the extent of this viewport, inherit the clipping region from the parent viewport, or turn clipping off altogether. For back-compatibility, a logical value of TRUE corresponds to "on" and FALSE corresponds to "inherit".

May also be a grob (or a gTree) that describes a clipping path or the result of a call to as.path.

mask

One of "none" (or FALSE) or "inherit" (or TRUE) or a grob (or a gTree) or the result of call to as.mask. This specifies that the viewport should have no mask, or it should inherit the mask of its parent, or it should have its own mask, as described by the grob.

xscale

A numeric vector of length two indicating the minimum and maximum on the x-scale. The limits may not be identical.

yscale

A numeric vector of length two indicating the minimum and maximum on the y-scale. The limits may not be identical.

angle

A numeric value indicating the angle of rotation of the viewport. Positive values indicate the amount of rotation, in degrees, anticlockwise from the positive x-axis.

layout

A Grid layout object which splits the viewport into subregions.

layout.pos.row

A numeric vector giving the rows occupied by this viewport in its parent's layout.

layout.pos.col

A numeric vector giving the columns occupied by this viewport in its parent's layout.

name

A character value to uniquely identify the viewport once it has been pushed onto the viewport tree.

A data frame with at least 3 columns: chromosome, start, and end.

• Column 1: character or factor, chromosome name.

• Column 2: numeric, start position (must be <= end).

• Column 3: numeric, end position.

Numeric, the width of each window (default is 1e+07). Ignored if n_window is specified.

Integer, the number of windows per chromosome. If provided, overrides window_size and evenly splits the chromosome into n_window (non-overlapping) or 2*n_window - 1 (overlapping) windows.

Logical, whether to use overlapping windows (default TRUE). Overlapping windows are spaced by half the window size.

Character, either "coverage" or "count":

• "count": reports the number of regions overlapping each window.

• "coverage": reports the fraction of each window covered by regions.

Optional named vector of chromosome lengths. If missing, the maximum end value in the input is used as the chromosome length.

A data frame with at least 3 columns: chromosome, start, and end.

How to assign distance for intermediate regions: one of "min", "max", "mean", "left", or "right".

Either a grob object or a function (can be purrr-style) that accepts at least one argument (a data frame of transformed coordinates) and returns a grob.

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.

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)).

A single string of "group" or "panel", "group" draws geoms with draw_group, which displays multiple observations as one geometric object, and "panel" draws geoms with draw_panel, displaying individual graphical objects for each observation (row). Default: "group".

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

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.

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)).

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

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.

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)).

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

These dots are for future extensions and must be empty.

A function (purrr-style formula is accepted) that takes an image_read() object as input and returns an object compatible with as.raster(). You can use any of the ⁠image_*()⁠ functions from the magick package to process the raster image.

Additional arguments passed on to magick

A logical value indicating whether to linearly interpolate the image (the alternative is to use nearest-neighbour interpolation, which gives a more blocky result).

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

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.

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)).

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

A single boolean value indicates clockwise or not.

An integer indicating the number of steps to generate the pie chart radian. Increasing this value results in a smoother pie circular.

Line end style (round, butt, square).

Line join style (round, mitre, bevel).

Line mitre limit (number greater than 1).

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

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.

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)).

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

Line end style (round, butt, square).

Line join style (round, mitre, bevel).

Line mitre limit (number greater than 1).

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

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.

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)).

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

• A Stat ggproto subclass, for example StatCount.

• A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

• For more information and other ways to specify the stat, see the layer stat documentation.

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

• The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

• A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

• For more information and other ways to specify the position, see the layer position documentation.

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

• Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

• When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

• Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

• The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

A single boolean value indicates whether we should arrange the divided rectangles in the row-major order.

A single positive integer specifying the number of rows or columns in the layout of the subdivided cell. By default, the layout dimensions are determined automatically using logic similar to facet_wrap().

Line end style (round, butt, square).

Line join style (round, mitre, bevel).

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

A string specifying the arrangement direction:

• "h"(horizontal): Creates a single row (one-row layout).

• "v"(vertical): Creates a single column (one-column layout).

The following options can be used:

• NULL: No data is set.

• waiver(): Inherits the data from the layout matrix.

• A function (including purrr-like lambda syntax): Applied to the layout matrix to transform the data before use. To transform the final plot data, please use scheme_data().

• A matrix, data.frame, or atomic vector.

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

<dyn-dots> Additional arguments passed to fortify_data_frame().

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

Please add theme() directly to the ggplot instead.

An object to be converted into a grob.

Data used, typically inherited from the layout quad_layout()/ggheatmap() or stack_layout() object.

A string specifying the particular data to retrieve from the attached attribute. If NULL, the entire attached attribute list will be returned.

A boolean indicating whether to check if the field exists. If TRUE, an error will be raised if the specified field does not exist.

Input data for the layout.

<dyn-dots> A list of data to be attached.

A character vector representing the attached levels.

A quad_layout()/ggheatmap() or stack_layout() object.

Arguments passed to methods.

A string of "top", "left", "bottom", or "right".

A single number or string of the plot elements in the stack layout.

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

Please add theme() directly to the ggplot instead.

The following options can be used:

• NULL: No data is set.

• waiver(): Inherits the data from the layout matrix.

• A function (including purrr-like lambda syntax): Applied to the layout matrix to transform the data before use. To transform the final plot data, please use scheme_data().

• A matrix, data.frame, or atomic vector.

<dyn-dots> Additional arguments passed to fortify_data_frame().

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

A mark_draw() object to define how to draw the links. Like mark_line(), mark_tetragon(). Note the names of the pair links will be used to define the panel names so must be unique.

The following options can be used:

• NULL: No data is set.

• waiver(): Inherits the data from the layout matrix.

• A function (including purrr-like lambda syntax): Applied to the layout matrix to transform the data before use. To transform the final plot data, please use scheme_data().

• A matrix, data.frame, or atomic vector.

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

<dyn-dots> Additional arguments passed to fortify_data_frame().

A single boolean value indicating whether to use the panel group information from the layout as the paired groups. By default, if no specific observations are selected in mark, ggmark() will automatically connect all observations and group them according to the layout's defined groups.

A single numeric value that indicates the size of a single observation, ranging from ⁠(0, 1]⁠.

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

A active() object that defines the context settings when added to a layout.

A character matrix which encodes the alterations, you can use ";", ":", ",", or "|" to separate multiple alterations.

Default list of aesthetic mappings to use for main plot in the layout. If not specified, must be supplied in each layer added to the main plot.

Additional arguments passed to fortify_matrix().

A named numeric value defines the width/height of each alterations.

A boolean value indicating whether to reorder the rows based on the frequency of alterations. You can set this to FALSE, then add align_order(~rowSums(!is.na(.x)), reverse = TRUE) to achieve the same result. You may also need to set strit = FALSE in align_order() if there are already groups.

A boolean value indicating whether to reorder the columns based on the characteristics of the alterations. You can set this to FALSE, then add align_order2(memo_order) to achieve the same result. You may also need to set strit = FALSE in align_order2() if there are already groups.

A logical value indicating whether to remove duplicated variants within the same cell.

The relative width/height of the main plot, can be a unit object.

Same as ggheatmap(), but only "tile" can be used.

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

A active() object that defines the context settings when added to a layout.

Data used to create the UpSet plot. fortify_matrix() will be used to convert the data to a matrix. Currently, only fortify_matrix.list_upset and fortify_matrix.matrix_upset are suitable for creating an UpSet plot.

Default list of aesthetic mappings to use for main plot in the layout. If not specified, must be supplied in each layer added to the main plot.

Additional arguments passed to fortify_matrix().

A string indicating the direction of the UpSet plot, "h"(horizontal) or "v"(vertical). In a vertical UpSet plot, the columns of the matrix correspond to the sets, and the rows correspond to the intersections. By default, the horizontal UpSet plot is used, where the rows of the matrix correspond to the sets and the columns correspond to the intersections.

A list of parameters passed to geom_point().

A list of parameters passed to geom_line().

A list of parameters passed to geom_rect().

The relative width/height of the main plot, can be a unit object.

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

A active() object that defines the context settings when added to a layout.

Any graphic that can be converted into a grob using patch().

Additional arguments passed to the patch() method.

A string specifying the area to place the plot: "full" for the full area, "plot" for the full plotting area (including the axis label), or "panel" for only the actual area where data is drawn.

A single boolean value indicates whether the graphic plot should be put frontmost. Note: the graphic plot will always put above the background.

A single boolean value indicating whether the grob should be clipped if they expand outside their designated area.

A viewport object, you can use this to define the plot area.

A numeric matrix, or data frame.

A string of distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Correlation coefficient can be also used, including "pearson", "spearman" or "kendall". In this way, 1 - cor will be used as the distance. In addition, you can also provide a dist object directly or a function return a dist object. Use NULL, if you don't want to calculate the distance.

A string of the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). You can also provide a function which accepts the calculated distance (or the input matrix if distance is NULL) and returns a hclust object. Alternative, you can supply an object which can be coerced to hclust.

An optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs". Only used when distance is a correlation coefficient string.

Default dataset to use for the layout. If not specified, it must be supplied in each plot added to the layout. By default, it will try to inherit from parent layout. fortify_matrix() will be used to convert data to a matrix.

Default list of aesthetic mappings to use for main plot in the layout. If not specified, must be supplied in each layer added to the main plot.

Additional arguments passed to fortify_matrix().

The relative width/height of the main plot, can be a unit object.

A single string of "raster" or "tile" to indicate the filling style. By default, waiver() is used, which means that if the input matrix has more than 20,000 cells (nrow * ncol > 20000), geom_raster() will be used for performance efficiency; for smaller matrices, geom_tile() will be used. To customize the filling style, set this to NULL.

For backward compatibility, a single boolean value is acceptable: TRUE means waiver(), and FALSE means NULL.

By default, the classic heatmap color scheme scale_fill_gradient2(low = "blue", high = "red") is utilized for continuous values.

You can use the options "ggalign.heatmap_continuous_fill" or "ggalign.heatmap_discrete_fill" to modify the default heatmap body filling color scale. See scale_fill_continuous() or scale_fill_discrete() for details on option settings.

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

A active() object that defines the context settings when added to a layout.

Any graphic that can be converted into a grob using patch().

Additional arguments passed to the patch() method.

A string specifying the area to place the plot: "full" for the full area, "plot" for the full plotting area (including the axis label), or "panel" for only the actual area where data is drawn.

A single boolean value indicates whether the graphic plot should be put frontmost. Note: the graphic plot will always put above the background.

A single boolean value indicating whether the grob should be clipped if they expand outside their designated area.

A viewport object, you can use this to define the plot area.

An object to test.

A layer geometry object to be added.

An integer indicating the position at which the layer should be added. If ⁠<= 0⁠, the layer will be added at the beginning. If greater than the number of plot layers, it will be added at the end.

A quad_layout()/ggheatmap() or stack_layout() object.

An object to be added to the plot.

Currently unused. May accept a theme in the future.

A theme object. If not waiver(), an error will be raised.

The dimensions of the grid to create - if both are NULL it will use the same logic as facet_wrap() to set the dimensions

If FALSE the plots will be filled in in column-major order.

The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid. The special value of NA will behave as ⁠1null⁠ unit unless a fixed aspect plot is inserted in which case it will allow the dimension to expand or contract to match the aspect ratio of the content.

Specification of the location of areas in the layout. Can either be specified as a text string or by concatenating calls to area() together.

A string with one or more of "t", "l", "b", "r", and "i" indicating which side of guide legends should be collected. Defaults to waiver(), which inherits from the parent layout. If there is no parent layout, or if NULL is provided, no guides will be collected.

An alias for area, retained for backward compatibility.

A list of range expansion constants, used to add padding around the data to ensure they are placed some distance away from the axes. Use the convenience function expansion() to generate the values.

Same as ..., but specifically for quad_layout().

Tag templates for plots in the layout. If waiver() (default), tags are inherited from the parent layout. If there is no parent layout, no tags are applied.

If NULL, tags are suppressed for this layout. In a nested layout, the parent layout's tag is applied to the the entire layout as a single unit.

If not NULL, must be one of:

• A character vector specifying explicit tags for each plot, or

• A single character indicating an auto-generated sequence:

  • 'a': lowercase letters

  • 'A': uppercase letters

  • '1': numbers

  • 'i': lowercase Roman numerals

  • 'I': uppercase Roman numerals

When a parent layout exists, each plot's tag is prefixed with the parent tag and separated by sep.

Separator between the parent tag (without its own prefix and suffix) and the current tag.

String prepended to the tag.

String appended to the tag.

A theme() object or additional element specifications not part of base ggplot2. In general, these should also be defined in the ⁠element tree⁠ argument. Splicing a list is also supported.

all line elements (element_line())

all rectangular elements (element_rect())

all text elements (element_text())

all title elements: plot, axes, legends (element_text(); inherits from text)

all point elements (element_point())

all polygon elements (element_polygon())

defaults for geoms (element_geom())

all spacings (unit())

all margins (margin())

aspect ratio of the panel

labels of axes (element_text()). Specify all axes' labels (axis.title), labels by plane (using axis.title.x or axis.title.y), or individually for each axis (using axis.title.x.bottom, axis.title.x.top, axis.title.y.left, axis.title.y.right). ⁠axis.title.*.*⁠ inherits from ⁠axis.title.*⁠ which inherits from axis.title, which in turn inherits from text

tick labels along axes (element_text()). Specify all axis tick labels (axis.text), tick labels by plane (using axis.text.x or axis.text.y), or individually for each axis (using axis.text.x.bottom, axis.text.x.top, axis.text.y.left, axis.text.y.right). ⁠axis.text.*.*⁠ inherits from ⁠axis.text.*⁠ which inherits from axis.text, which in turn inherits from text

tick marks along axes (element_line()). Specify all tick marks (axis.ticks), ticks by plane (using axis.ticks.x or axis.ticks.y), or individually for each axis (using axis.ticks.x.bottom, axis.ticks.x.top, axis.ticks.y.left, axis.ticks.y.right). ⁠axis.ticks.*.*⁠ inherits from ⁠axis.ticks.*⁠ which inherits from axis.ticks, which in turn inherits from line

minor tick marks along axes (element_line()). ⁠axis.minor.ticks.*.*⁠ inherit from the corresponding major ticks ⁠axis.ticks.*.*⁠.

length of tick marks (unit). axis.ticks.length inherits from spacing.

length of minor tick marks (unit), or relative to axis.ticks.length when provided with rel().

lines along axes (element_line()). Specify lines along all axes (axis.line), lines for each plane (using axis.line.x or axis.line.y), or individually for each axis (using axis.line.x.bottom, axis.line.x.top, axis.line.y.left, axis.line.y.right). ⁠axis.line.*.*⁠ inherits from ⁠axis.line.*⁠ which inherits from axis.line, which in turn inherits from line

background of legend (element_rect(); inherits from rect)

the margin around each legend (margin()); inherits from margins.

the spacing between legends (unit). legend.spacing.x & legend.spacing.y inherit from legend.spacing or can be specified separately. legend.spacing inherits from spacing.

background underneath legend keys (element_rect(); inherits from rect)

size of legend keys (unit); key background height & width inherit from legend.key.size or can be specified separately. In turn legend.key.size inherits from spacing.

spacing between legend keys given as a unit. Spacing in the horizontal (x) and vertical (y) direction inherit from legend.key.spacing or can be specified separately. legend.key.spacing inherits from spacing.

Justification for positioning legend keys when more space is available than needed for display. The default, NULL, stretches keys into the available space. Can be a location like "center" or "top", or a two-element numeric vector.

frame drawn around the bar (element_rect()).

tick marks shown along bars or axes (element_line())

length of tick marks in legend (unit()); inherits from legend.key.size.

lines along axes in legends (element_line())

legend item labels (element_text(); inherits from text)

placement of legend text relative to legend keys or bars ("top", "right", "bottom" or "left"). The legend text placement might be incompatible with the legend's direction for some guides.

title of legend (element_text(); inherits from title)

placement of legend title relative to the main legend ("top", "right", "bottom" or "left").

the default position of legends ("none", "left", "right", "bottom", "top", "inside")

A numeric vector of length two setting the placement of legends that have the "inside" position.

layout of items in legends ("horizontal" or "vertical")

whether the legend-matrix is filled by columns (FALSE, the default) or by rows (TRUE).

anchor point for positioning legend inside plot ("center" or two-element numeric vector) or the justification according to the plot area when positioned outside the plot

Same as legend.justification but specified per legend.position option.

Relative placement of legends outside the plot as a string. Can be "panel" (default) to align legends to the panels or "plot" to align legends to the plot as a whole.

arrangement of multiple legends ("horizontal" or "vertical")

justification of each legend within the overall bounding box, when there are multiple legends ("top", "bottom", "left", "right", "center" or "centre")

margins around the full legend area, as specified using margin(); inherits from margins.

background of legend area (element_rect(); inherits from rect)

The spacing between the plotting area and the legend box (unit); inherits from spacing.

background of plotting area, drawn underneath plot (element_rect(); inherits from rect)

border around plotting area, drawn on top of plot so that it covers tick marks and grid lines. This should be used with fill = NA (element_rect(); inherits from rect)

spacing between facet panels (unit). panel.spacing.x & panel.spacing.y inherit from panel.spacing or can be specified separately. panel.spacing inherits from spacing.

grid lines (element_line()). Specify major grid lines, or minor grid lines separately (using panel.grid.major or panel.grid.minor) or individually for each axis (using panel.grid.major.x, panel.grid.minor.x, panel.grid.major.y, panel.grid.minor.y). Y axis grid lines are horizontal and x axis grid lines are vertical. ⁠panel.grid.*.*⁠ inherits from ⁠panel.grid.*⁠ which inherits from panel.grid, which in turn inherits from line

option to place the panel (background, gridlines) over the data layers (logical). Usually used with a transparent or blank panel.background.

Sizes for panels (units). Can be a single unit to set the total size for the panel area, or a unit vector to set the size of individual panels.

background of the entire plot (element_rect(); inherits from rect)

plot title (text appearance) (element_text(); inherits from title) left-aligned by default

Alignment of the plot title/subtitle and caption. The setting for plot.title.position applies to both the title and the subtitle. A value of "panel" (the default) means that titles and/or caption are aligned to the plot panels. A value of "plot" means that titles and/or caption are aligned to the entire plot (minus any space for margins and plot tag).

plot subtitle (text appearance) (element_text(); inherits from title) left-aligned by default

caption below the plot (text appearance) (element_text(); inherits from title) right-aligned by default

upper-left label to identify a plot (text appearance) (element_text(); inherits from title) left-aligned by default

The position of the tag as a string ("topleft", "top", "topright", "left", "right", "bottomleft", "bottom", "bottomright") or a coordinate. If a coordinate, can be a numeric vector of length 2 to set the x,y-coordinate relative to the whole plot. The coordinate option is unavailable for plot.tag.location = "margin".

The placement of the tag as a string, one of "panel", "plot" or "margin". Respectively, these will place the tag inside the panel space, anywhere in the plot as a whole, or in the margin around the panel space.

margin around entire plot (unit with the sizes of the top, right, bottom, and left margins); inherits from margin.

background of facet labels (element_rect(); inherits from rect). Horizontal facet background (strip.background.x) & vertical facet background (strip.background.y) inherit from strip.background or can be specified separately

should strip background edges and strip labels be clipped to the extend of the strip background? Options are "on" to clip, "off" to disable clipping or "inherit" (default) to take the clipping setting from the parent viewport.

placement of strip with respect to axes, either "inside" or "outside". Only important when axes and strips are on the same side of the plot.

facet labels (element_text(); inherits from text). Horizontal facet labels (strip.text.x) & vertical facet labels (strip.text.y) inherit from strip.text or can be specified separately. Facet strips have dedicated position-dependent theme elements (strip.text.x.top, strip.text.x.bottom, strip.text.y.left, strip.text.y.right) that inherit from strip.text.x and strip.text.y, respectively. As a consequence, some theme stylings need to be applied to the position-dependent elements rather than to the parent elements

space between strips and axes when strips are switched (unit); inherits from spacing.

set this to TRUE if this is a complete theme, such as the one returned by theme_grey(). Complete themes behave differently when added to a ggplot object. Also, when setting complete = TRUE all elements will be set to inherit from blank elements.

TRUE to run check_element(), FALSE to bypass checks.

The text for the title.

The text for the subtitle for the plot which will be displayed below the title.

The text for the caption which will be displayed in the bottom-right of the plot by default.

A function used to draw the links. The function must return a grob() object. If the function does not return a valid grob, no drawing will occur. The input data for the function must contain two arguments: a data frame for the left hand coordinates and a data frame for the right hand observation coordinates.

<dyn-dots> A list of formulas, where each side of the formula should be an integer or character index of the original data, or a range_link() object defining the linked observations. Use NULL to indicate no link on that side. You can also combine these by wrapping them into a single list(). If only the left-hand side of the formula exists, you can input it directly. For integer indices, wrap them with I() to use the ordering from the layout. You can also use waiver() to inherit values from the other group.

<dyn-dots> A list of formulas, where each side of the formula should be an integer or character index of the original data, or a range_link() object defining the linked observations. Use NULL to indicate no link on that side. You can also combine these by wrapping them into a single list(). If only the left-hand side of the formula exists, you can input it directly. For integer indices, wrap them with I() to use the ordering from the layout. You can also use waiver() to inherit values from the other group.

A element_line() object. Vectorized fields will be recycled to match the total number of groups, or you can wrap the element with I() to recycle to match the drawing groups. The drawing groups typically correspond to the product of the number of observations from both sides, as each pair of observations will be linked with a single line.

<dyn-dots> A list of formulas, where each side of the formula should be an integer or character index of the original data, or a range_link() object defining the linked observations. Use NULL to indicate no link on that side. You can also combine these by wrapping them into a single list(). If only the left-hand side of the formula exists, you can input it directly. For integer indices, wrap them with I() to use the ordering from the layout. You can also use waiver() to inherit values from the other group.