Plot a dimensionality reduced trajectory as a 2D graph

Plot a dimensionality reduced trajectory as a 2D graph

plot_graph(traj, 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, transition_size = 3,
  milestone_size = 5, arrow_length = grid::unit(1, "cm"),
  label_milestones = dynwrap::is_wrapper_with_milestone_labelling(traj),
  plot_milestones = TRUE)

Arguments

traj	The trajectory
color_cells	How to color the cells
color_milestones	How to color the cells
grouping	The grouping of the cells
groups	Tibble containing information of the cell groups
feature_oi	feature to plot expression
pseudotime	The pseudotime
expression_source	Source of the feature expression, defaults to `expression`
milestones	Tibble containing the `milestone_id` and a `color` for each milestone
milestone_percentages	The milestone percentages
transition_size	The size of the transition lines between milestones.
milestone_size	The size of milestones.
arrow_length	length of the arrow.
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.