plotTreeDual: Plot 2D Dendrogram of URD Tree

In farrellja/URD: URD

Description

Plot 2D Dendrogram of URD Tree

Usage

plotTreeDual(
  object,
  label.red,
  label.green,
  label.type.red = "search",
  label.type.green = "search",
  title = NULL,
  legend = T,
  legend.title = "",
  plot.tree = T,
  tree.alpha = 1,
  tree.size = 1,
  plot.cells = T,
  cell.alpha = 0.25,
  cell.size = 0.5,
  label.x = T,
  label.segments = F,
  color.tree = T,
  color.limits.red = NULL,
  color.limits.green = NULL,
  hide.y.ticks = T
)

Arguments

object	An URD object
label.red	(Character) Data to use for coloring points/tree in the red channel: see data.for.plot
label.green	(Character) Data to use for coloring points/tree in the green channel: see data.for.plot
label.type.red	(Character) Type of data to search for the label for the red channel. Default is "search" which checks several data types in order. For more information: data.for.plot
label.type.green	(Character) Type of data to search for the label for the green channel. Default is "search" which checks several data types in order. For more information: data.for.plot
title	(Character) Title to display on the plot. Default NULL auto-creates a title based on what is plotted.
legend	(Logical) Show a legend?
legend.title	(Character) Title to display on the legend
plot.tree	(Logical) Whether cells should be plotted with the tree
tree.alpha	(Numeric) Transparency of dendrogram (0 is transparent, 1 is opaque)
tree.size	(Numeric) Thickness of lines of dendrogram
cell.alpha	(Numeric) Transparency of cells (0 is transparent, 1 is opaque)
cell.size	(Numeric) How large should cells be
label.x	(Logical) Should tips on the x-axis be labeled
label.segments	(Logical) Should segments of the dendrogram be labeled with their numbers
color.tree	(Logical) Should the dendrogram be colored according to the data?
color.limits.red	(Numeric vector, length 2) Minimum and maximum values for color scale. Default NULL auto-detects.
color.limits.green	(Numeric vector, length 2) Minimum and maximum values for color scale. Default NULL auto-detects.
hide.y.ticks	(Logical) Should the pseudotime values on the y-axis be hidden?

Value

A ggplot2 object

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