SingleAnnotation: Constructor method for SingleAnnotation class
In eilslabs/ComplexHeatmap: Making Complex Heatmaps

Description Usage Arguments Details Value Author(s) See Also Examples

Constructor method for SingleAnnotation class

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))

`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)`.

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.

A SingleAnnotation-class object.

Zuguang Gu <z.gu@dkfz.de>

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.

# 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))