plotTreeHighlight: Plot 2D Dendrogram of URD Tree (with cells that meet...

In farrellja/URD: URD

Description

This produces an URD dendrogram with cells that meet any group of arbitrary criteria highlighted on the tree. It uses the highlight.cells, highlight.cells.alpha, and highlight.cells.size parameters of plotTree which can alternatively be used to accomplish this.

Usage

plotTreeHighlight(
  object,
  label.name,
  label.value,
  color = "red",
  bg.color = "#CCCCCC",
  highlight.alpha = 0.6,
  highlight.size = 1.5,
  combine = c("intersect", "union"),
  ...
)

Arguments

object	An URD object
label.name	(Character vector) Data to use for selecting cells, see data.for.plot
label.value	(List of vectors) List of same length as label.name; Each entry is the acceptable values for the corresponding entry in label.name
color	(Character) Color to use for highlighted cells
bg.color	(Character) Color to use for non-highlighted cells
highlight.alpha	(Numeric) Transparency of highlighted cells (0 is fully transparent, 1 is fully opaque)
highlight.size	(Numeric) Size of points of highlighted cells
combine	(Character) Should highlighted cells be the intersect (i.e. cells that meet ALL criteria) or the union (i.e. cells that meet any criteria)
...	all additional parameters are passed to plotTree

Value

A ggplot2 object

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.