Description Usage Arguments Value
Plot 2D Dendrogram of URD Tree
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | 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
)
|
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 |
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 |
symmetric.color.scale |
(Logical) Should the color scale be symmetric and centered around 0? (Default |
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 |
A ggplot2 object
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