Link annotation with labels

Link annotation with labels

anno_mark(at, labels, which = c("column", "row"),
    side = ifelse(which == "column", "top", "right"),
    lines_gp = gpar(), labels_gp = gpar(),
    labels_rot = ifelse(which == "column", 90, 0), padding = 0.5,
    link_width = unit(5, "mm"), link_height = link_width,
    link_gp = lines_gp,
    extend = unit(0, "mm"))

Arguments

at

Numeric index from the original matrix.
labels

Corresponding labels.
which

Whether it is a column annotation or a row annotation?
side

Side of the labels. If it is a column annotation, valid values are "top" and "bottom"; If it is a row annotation, valid values are "left" and "right".
lines_gp

Please use link_gp instead.
link_gp

Graphic settings for the segments.
labels_gp

Graphic settings for the labels.
labels_rot

Rotations of labels, scalar.
padding

Padding between neighbouring labels in the plot.
link_width

Width of the segments.
link_height

Similar as link_width, used for column annotation.
extend

By default, the region for the labels has the same width (if it is a column annotation) or same height (if it is a row annotation) as the heatmap. The size can be extended by this options. The value can be a proportion number or a unit object. The length can be either one or two.

Details

Sometimes there are many rows or columns in the heatmap and we want to mark some of the rows. This annotation function is used to mark these rows and connect labels and corresponding rows with links.

Value

An annotation function which can be used in HeatmapAnnotation.

See also

https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#mark-annotation

Examples

anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
draw(anno, index = 1:100, test = "anno_mark")

m = matrix(1:1000, byrow = TRUE, nr = 100)
anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
Heatmap(m, cluster_rows = FALSE, cluster_columns = FALSE) + rowAnnotation(mark = anno)
Heatmap(m) + rowAnnotation(mark = anno)