plot_graph: Plot a trajectory as a graph

In dynplot: Visualising Single-Cell Trajectories

Description

Plot a trajectory as a graph

Usage

plot_graph(
  trajectory,
  color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"),
  color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"),
  grouping = NULL,
  groups = NULL,
  feature_oi = NULL,
  pseudotime = NULL,
  expression_source = "expression",
  milestones = NULL,
  milestone_percentages = NULL,
  size_trajectory = 3,
  size_milestones = 8,
  alpha_cells = 1,
  size_cells = 2.5,
  border_radius_percentage = 0.1,
  arrow = grid::arrow(length = grid::unit(1, "cm"), type = "closed"),
  label_milestones = dynwrap::is_wrapper_with_milestone_labelling(trajectory),
  plot_milestones = FALSE,
  adjust_weights = FALSE
)

Arguments

trajectory	The trajectory as created by infer_trajectory() or add_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.
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.
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).
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.
size_trajectory	The size of the transition lines between milestones.
size_milestones	The size of milestones.
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.
arrow	The type and size of arrow in case of directed trajectories. Set to NULL to remove arrow altogether.
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
plot_milestones	Whether to plot the milestones.
adjust_weights	Whether or not to rescale the milestone network weights

Value

A graph ggplot of a trajectory.

Examples

data(example_disconnected)
plot_graph(example_disconnected)
plot_graph(example_disconnected, color_cells = "pseudotime")
plot_graph(
  example_disconnected,
  color_cells = "grouping",
  grouping = dynwrap::group_onto_nearest_milestones(example_disconnected)
)

data(example_tree)
plot_graph(example_tree)

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