dynplot (version 1.1.2)

plot_dendro: Plot a trajectory as a dendrogram

Description

Plot a trajectory as a dendrogram

Usage

plot_dendro(
  trajectory,
  color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"),
  grouping = NULL,
  groups = NULL,
  feature_oi = NULL,
  expression_source = "expression",
  pseudotime = NULL,
  color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"),
  milestones = NULL,
  milestone_percentages = NULL,
  alpha_cells = 1,
  size_cells = 2.5,
  border_radius_percentage = 0.1,
  diag_offset = 0.05,
  y_offset = 0.2,
  arrow = grid::arrow(type = "closed")
)

Arguments

trajectory

A dynwrap trajectory.

color_cells

How to color the cells.

• "auto": Try to figure out how to color cells depending on whether one of the grouping, feature_io, milestones or pseudotime parameters are defined.

• "none": Cells are not coloured.

• "grouping": Cells are coloured according to a grouping (e.g. clustering). Either the grouping parameter or trajectory$grouping must be a named character vector.

• "feature": Cells are coloured according to the values of a given feature (e.g. gene expression). Either the expression_source parameter or get_expression(trajectory) must be a matrix. Parameter feature_oi must also be defined.

• "milestone" (recommended): Cells are coloured according their position in the trajectory. The positioning of the cells are determined by parameter milestone_percentages or else by trajectory$milestone_percentages. The colours of the milestones can be determined automatically or can be specified by passing a tibble containing character columns milestone_id and color (See add_milestone_coloring() for help in constructing this object).

• "pseudotime": Cells are coloured according to the pseudotime value from the root.

grouping

A grouping of the cells (e.g. clustering) as a named character vector.

groups

A tibble containing character columns group_id and color. If NULL, this object is inferred from the grouping itself.

feature_oi

The name of a feature to use for colouring the cells.

expression_source

Source of the feature expression, defaults to get_expression(trajectory).

pseudotime

The pseudotime from the root of the trajectory to the cells as a named numeric vector.

color_milestones

Which palette to use for colouring the milestones

• auto: Determine colours automatically. If color is already specified in milestones tibble, this will be used. Otherwise, the colour scheme is determined by milestone_palette_list$auto.

• given: The milestones object already contains a column color.

• cubeHelix: Use the rje::cubeHelix() palette.

• Set3: Use the RColorBrewer::brewer.pal(name = "Set3") palette.

• rainbow: Use the grDevices::rainbow() palette.

milestones

Tibble containing the column milestone_id (character). If color_milestones is set to "given", this tibble should also contain a column color (character), containing colour hex codes (e.g. "#123456").

milestone_percentages

The milestone percentages.

alpha_cells

The alpha of the cells

size_cells

The size of the cells

border_radius_percentage

The fraction of the radius that is used for the border

diag_offset

The x-offset (percentage of the edge lenghts) between milestones

y_offset

The size of the quasirandom cell spreading in the y-axis

arrow

The type and size of arrow in case of directed trajectories. Set to NULL to remove arrow altogether.

Value

A dendrogram ggplot of the trajectory.

Examples

# NOT RUN {
data(example_tree)
plot_dendro(example_tree)
plot_dendro(example_tree, color_cells = "pseudotime")
plot_dendro(
  example_tree,
  color_cells = "grouping",
  grouping = dynwrap::group_onto_nearest_milestones(example_tree)
)
# }