anno_density: Density Annotation
In ComplexHeatmap: Make Complex Heatmaps

Description Usage Arguments Value See Also Examples

View source: R/AnnotationFunction-function.R

Density Annotation

anno_density(x, which = c("column", "row"),
    type = c("lines", "violin", "heatmap"), xlim = NULL,
    heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)),
    joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),
    axis = TRUE, axis_param = default_axis_param(which),
    width = NULL, height = NULL)

`x`	A matrix or a list. If `x` is a matrix and if `which` is `column`, statistics for boxplots are calculated by columns, if `which` is `row`, the calculation is done by rows.
`which`	Whether it is a column annotation or a row annotation?
`type`	Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot and "heatmap" for heatmap visualization of density distribution.
`xlim`	Range on x-axis.
`heatmap_colors`	A vector of colors for interpolating density values.
`joyplot_scale`	Relative height of density distribution. A value higher than 1 increases the height of the density distribution and the plot will represented as so-called "joyplot".
`border`	Wether draw borders of the annotation region?
`gp`	Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations.
`axis`	Whether to add axis?
`axis_param`	parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.
`width`	Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
`height`	Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.

An annotation function which can be used in HeatmapAnnotation.

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

m = matrix(rnorm(100), 10)
anno = anno_density(m, which = "row")
draw(anno, test = "normal density")
anno = anno_density(m, which = "row", type = "violin")
draw(anno, test = "violin")
anno = anno_density(m, which = "row", type = "heatmap")
draw(anno, test = "heatmap")
anno = anno_density(m, which = "row", type = "heatmap", 
    heatmap_colors = c("white", "orange"))
draw(anno, test = "heatmap, colors")

Loading required package: grid
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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))
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