> Reference > > dynplot :: Plot a trajectory > Plot a trajectory and cellular positions as a graph

Plot a trajectory and cellular positions as a graph

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, transition_size = 3,
  milestone_size = 5, arrow_length = grid::unit(1, "cm"),
  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
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.
adjust_weights	Whether or not to rescale the milestone network weights

Examples

data(example_disconnected)
plot_graph(example_disconnected)
#> Coloring by milestone
#> Using milestone_percentages from trajectory
plot_graph(example_disconnected, color_cells = "pseudotime")
#> Pseudotime not provided, will calculate pseudotime from root milestone
#> root cell or milestone not provided, trying first outgoing milestone_id
#> Using 'T1_M4' as root
plot_graph(
  example_disconnected,
  color_cells = "grouping",
  grouping = dynwrap::group_onto_nearest_milestones(example_disconnected)
)
data(example_tree)
plot_graph(example_tree)
#> Coloring by milestone
#> Using milestone_percentages from trajectory