SingleAnnotation: Constructor Method for SingleAnnotation Class
In zhongmicai/complexHeatmap: Make 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),
    border = FALSE,
    legend_param = list(),
    show_name = TRUE,
    name_gp = gpar(fontsize = 12),
    name_offset = NULL,
    name_side = ifelse(which == "column", "right", "bottom"),
    name_rot = NULL,
    simple_anno_size = ht_opt$simple_anno_size,
    width = NULL, height = NULL)

`name`	Name for the annotation. If it is not specified, an internal name is assigned.
`value`	A vector or a matrix of discrete or continuous values.
`col`	Colors corresponding to `value`. If the mapping is discrete, the value of `col` should be a named vector; If the mapping is continuous, the value of `col` should be a color mapping function.
`fun`	A user-defined function to add annotation graphics. The argument of this function should be at least a vector of index that corresponds to rows or columns. Normally the function should be constructed by `AnnotationFunction` if you want the annotation supports splitting. See Details for more explanation.
`na_col`	Color for `NA` values in the simple annotations.
`which`	Whether the annotation is a row annotation or a column annotation?
`show_legend`	If it is a simple annotation, whether show legend in the final heatmap?
`gp`	Since simple annotation is represented as rows of grids. This argument controls graphic parameters for the simple annotation. The `fill` parameter is ignored here.
`border`	border, only work for simple annotation
`legend_param`	Parameters for the legend. See `color_mapping_legend,ColorMapping-method` for all possible 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, it can only take values in `c(0, 90, 180, 270)`.
`simple_anno_size`	size of the simple annotation.
`width`	The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit.
`height`	The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.

A single annotation is a basic unit of complex heatmap annotations where the heamtap annotations are always a list of single annotations. An annotation can be simply heatmap-like (here we call it simple annotation) or more complex like points, lines, boxes (for which we call it complex annotation).

In the SingleAnnotation constructor, value, col, na_col are used to construct a anno_simple annotation funciton which is generated internally by AnnotationFunction. The legend of the simple annotation can be automatcally generated,

For construcing a complex annotation, users need to use fun which is a user-defind function. Normally it is constucted by AnnotationFunction. One big advantage for using AnnotationFunction is the annotation function or the graphics drawn by the annotation function can be split according to row splitting or column splitting of the heatmap. Users can also provide a "pure" function which is a normal R function for the fun argument. The function only needs one argument which is a vector of index for rows or columns depending whether it is a row annotation or column annotation. The other two optional arguments are the current slice index and total number of slices. See **Examples** section for an example. If it is a normal R function, it will be constructed into the AnnotationFunction-class object internally.

The SingleAnnotation-class is a simple wrapper on top of AnnotationFunction-class only with annotation name added.

The class also stored the "extended area" relative to the area for the annotation graphics. The extended areas are those created by annotation names and axes.

A SingleAnnotation-class object.

Zuguang Gu <z.gu@dkfz.de>

There are following built-in annotation functions that can be directly used to generate complex annotations: anno_simple, anno_points, anno_lines, anno_barplot, anno_histogram, anno_boxplot, anno_density, anno_text, anno_joyplot, anno_horizon, anno_image, anno_block, anno_summary and anno_mark.

ha = SingleAnnotation(value = 1:10)
draw(ha, test = "single column annotation")

m = cbind(1:10, 10:1)
colnames(m) = c("a", "b")
ha = SingleAnnotation(value = m)
draw(ha, test = "matrix as column annotation")

anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)))
ha = SingleAnnotation(fun = anno)
draw(ha, test = "anno_barplot as input")

fun = local({
    # because there variables outside the function for use, we put it a local environment
    value = 1:10
    function(index, k = 1, n = 1) {
        pushViewport(viewport(xscale = c(0.5, length(index) + 0.5), yscale = range(value)))
        grid.points(seq_along(index), value[index])
        grid.rect()
        if(k == 1) grid.yaxis()
        popViewport()
    }
})
ha = SingleAnnotation(fun = fun, height = unit(4, "cm"))
draw(ha, index = 1:10, test = "self-defined function")