SingleAnnotation {ComplexHeatmap} | R Documentation

## Constructor method for SingleAnnotation class

### Description

Constructor method for SingleAnnotation class

### Usage

    SingleAnnotation(name, value, col, fun,
        na_col = "grey",
        which = c("column", "row"),
        show_legend = TRUE,
        gp = gpar(col = NA),
        legend_param = list(),
        show_name = FALSE,
        name_gp = gpar(fontsize = 12),
        name_offset = unit(2, "mm"),
        name_side = ifelse(which == "column", "right", "bottom"),
        name_rot = ifelse(which == "column", 0, 90))

### Arguments

`name` | name for this annotation. If it is not specified, an internal name is assigned.
`value` | A vector of discrete or continuous annotation.
`col` | colors corresponding to `value`. If the mapping is discrete mapping, the value of `col` should be a vector; If the mapping is continuous mapping, the value of `col` should be a color mapping function.
`fun` | a self-defined function to add annotation graphics. The argument of this function should only be a vector of index that corresponds to rows or columns.
`na_col` | color for `NA` values in simple annotations.
`which` | is the annotation a row annotation or a column annotation?
`show_legend` | if it is a simple annotation, whether show legend when making the complete heatmap.
`gp` | Since simple annotation is represented as a row of grids. This argument controls graphic parameters for the simple annotation.
`legend_param` | parameters for the legend. See `color_mapping_legend,ColorMapping-method` for options.
`show_name` | whether show annotation name
`name_gp` | graphic parameters for annotation name
`name_offset` | offset to the annotation, a `unit` object
`name_side` | 'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations
`name_rot` | rotation of the annotation name, can only take values in `c(00, 90, 180, 270)`.

### Details

The most simple annotation is one row or one column grids in which different colors represent different classes of the data. Here the function use `ColorMapping-class` to process such simple annotation. `value` and `col` arguments controls values and colors of the simple annotation and a `ColorMapping-class` object will be constructed based on `value` and `col`.

`fun` is used to construct a more complex annotation. Users can add any type of annotation graphics by implementing a function. The only input argument of `fun` is a index of rows or columns which is already adjusted by the clustering. In the package, there are already several annotation graphic function generators: `anno_points`, `anno_histogram` and `anno_boxplot`.

In the case that row annotations are splitted by rows, `index` corresponding to row orders in each row-slice and `fun` will be applied on each of the row slices.

One thing that users should be careful is the difference of coordinates when the annotation is a row annotation or a column annotation.

### Value

A `SingleAnnotation-class` object.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### See Also

There are following built-in annotation functions that can be used to generate complex annotations: `anno_points`, `anno_barplot`, `anno_histogram`, `anno_boxplot`, `anno_density`, `anno_text` and `anno_link`.

### Examples

    # discrete character
    SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"))
    SingleAnnotation(name = "test", value = c("a", "a", "a", "b", "b", "b"),
        which = "row")

    # with defined colors
    SingleAnnotation(value = c("a", "a", "a", "b", "b", "b"),
        col = c("a" = "red", "b" = "blue"))

    # continuous numbers
    require(circlize)
    SingleAnnotation(value = 1:10)
    SingleAnnotation(value = 1:10, col = colorRamp2(c(1, 10), c("blue", "red")))

    # self-defined graphic function
    SingleAnnotation(fun = anno_points(1:10))

[Package ComplexHeatmap version 1.18.1 Index]