plot_onedim: Plot a trajectory as a one-dimensional set of connected...

In dynplot: Visualising Single-Cell Trajectories

Description

Plot a trajectory as a one-dimensional set of connected segments

Usage

plot_onedim(
  trajectory,
  color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"),
  grouping = NULL,
  groups = NULL,
  feature_oi = NULL,
  pseudotime = NULL,
  expression_source = "expression",
  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,
  orientation = 1,
  margin = 0.05,
  linearised = linearise_cells(trajectory, margin, one_edge = TRUE),
  quasirandom_width = 0.2,
  plot_cells = TRUE,
  label_milestones = dynwrap::is_wrapper_with_milestone_labelling(trajectory),
  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.
pseudotime	The pseudotime from the root of the trajectory to the cells as a named numeric vector.
expression_source	Source of the feature expression, defaults to get_expression(trajectory).
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
orientation	Whether to plot the connections in the top (1) or bottom (-1)
margin	A margin between trajectory segments.
linearised	The linearised milestone network and progressions
quasirandom_width	The width of the quasirandom cell spreading
plot_cells	Whether to plot the cells
label_milestones	How to label the milestones. Can be TRUE (in which case the labels within the trajectory will be used), "all" (in which case both given labels and milestone_ids will be used), a named character vector, or FALSE
arrow	The type and size of arrow in case of directed trajectories. Set to NULL to remove arrow altogether.

Value

A linearised (non-)linear trajectory.

Examples

data(example_linear)
plot_onedim(example_linear)
plot_onedim(example_linear, label_milestones = TRUE)

data(example_tree)
plot_onedim(example_tree)

dynplot documentation built on Dec. 11, 2021, 9:33 a.m.