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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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dynverse/dynplot documentation built on Dec. 12, 2021, 9:39 p.m.