ComplexHeatmap (version 1.10.2)

SingleAnnotation: 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())

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.

Value

• A SingleAnnotation-class object.

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.

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))