plotTreeDiscretized: Plot 2D Dendrogram of URD Tree, Discretized
In farrellja/URD: URD

Description Usage Arguments Details Value

Plots cells on the URD 2D dendrogram. Cells are colored according to which of 1-3 labels are 'on' after conversion to discrete on/off values according to label.min and label.max. All labels must be continuous variables (i.e. not cluster identities).

plotTreeDiscretized(
  object,
  labels,
  label.types = rep("search", length(labels)),
  label.min = rep(0, length(labels)),
  label.max = rep(Inf, length(labels)),
  colors = c("grey", "blue", "green", "red", "cyan", "magenta", "yellow", "black"),
  title = NULL,
  tree.alpha = 1,
  tree.size = 1,
  tree.color = "grey",
  cell.alpha = 0.5,
  cell.size = 0.3,
  label.x = T,
  label.segments = F,
  hide.y.ticks = T
)

`object`	An URD object
`labels`	(Character vector, length 1-3) Data to plot
`label.types`	(Character vector, length 1-3) Type of data to search for the label for the first channel. Default is "search" which checks several data types in order. For more information: `data.for.plot`
`label.min`	(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between `label.min` and `label.max`
`label.max`	(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between `label.min` and `label.max`
`colors`	(Character vector) Colors to use for plotting. Color order is as follows: With one label (A): 1 A-, 2 A+; With two labels (A, B): 1 A- B-, 2 A+ B-, 3 A- B+, 4 A+ B+; With three labels (A, B, C): 1 A- B- C-, 2 A+ B- C-, 3 A- B+ C-, 4 A- B- C+, 5 A+ B+ C-, 6 A+ B- C+, 7 A- B+ C+, 8 A+ B+ C+
`title`	(Character) Title to display on the plot.
`tree.alpha`	(Numeric) Transparency of dendrogram (0 is transparent, 1 is opaque)
`tree.size`	(Numeric) Thickness of lines of dendrogram
`tree.color`	(Character) Color to use for tree lines
`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