anno_mark: Link annotation with labels

In ComplexHeatmap: Make Complex Heatmaps

Description

Link annotation with labels

Usage

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 = unit(1, "mm"),
    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)

Example output

Loading required package: grid
========================================
ComplexHeatmap version 2.6.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================

ComplexHeatmap documentation built on Nov. 14, 2020, 2:01 a.m.