plotTree: Plot 2D Dendrogram of URD Tree

In farrellja/URD: URD

Description

Plot 2D Dendrogram of URD Tree

Usage

plotTree(
  object,
  label = NULL,
  label.type = "search",
  title = label,
  legend = T,
  legend.title = "",
  legend.point.size = 6 * cell.size,
  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,
  discrete.ignore.na = F,
  color.tree = NULL,
  continuous.colors = NULL,
  discrete.colors = NULL,
  color.limits = NULL,
  symmetric.color.scale = NULL,
  hide.y.ticks = T,
  cells.highlight = NULL,
  cells.highlight.alpha = 1,
  cells.highlight.size = 2
)

Arguments

object	An URD object
label	(Character) Data to use for color information, see data.for.plot
label.type	(Character) See data.for.plot
title	(Character) Title to display on the plot
legend	(Logical) Show a legend?
legend.title	(Character) Title to display on the legend
legend.point.size	(Numeric) How big should points be in 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
discrete.ignore.na	(Logical)
color.tree	(Logical) Should the dendrogram be colored according to the data? Default NULL colors the tree when plotting continuous variables, but not when plotting discrete variables.
continuous.colors	(Character vector) Colors to make color scale if plotting a continuous variable
discrete.colors	(Character vector) Colors to use if plotting a discrete variable
color.limits	(Numeric vector, length 2) Minimum and maximum values for color scale. Default NULL auto-detects.
symmetric.color.scale	(Logical) Should the color scale be symmetric and centered around 0? (Default NULL is FALSE if all values are positive, and TRUE if both positive and negative values are present.)
hide.y.ticks	(Logical) Should the pseudotime values on the y-axis be hidden?
cells.highlight	(Character vector) Group of cells to plot last, ensuring that they are highlighted on the tree.
cells.highlight.alpha	(Numeric) Transparency of highlighted cells (0 is transparent, 1 is opaque)
cells.highlight.size	(Numeric) Size of highlighted cells

Value

A ggplot2 object

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