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).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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: |
label.min |
(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between |
label.max |
(Numeric vector, length 1-3) Consider a cell positive for a feature if its value is between |
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 |
Shamelessly inspired by the behavior of FeaturePlot in Seurat when overlay is turned on.
A ggplot2 object
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