SingleAnnotation: Constructor method for SingleAnnotation class

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

View source: R/SingleAnnotation-class.R

Description

Constructor method for SingleAnnotation class

Usage

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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 <[email protected]>

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

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# 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))

eilslabs/ComplexHeatmap documentation built on Oct. 19, 2017, 2:13 p.m.