> Reference > > dynplot :: Plot a trajectory > Plot a trajectory on dimensionality reduction

Plot a trajectory on dimensionality reduction

plot_dimred(trajectory, color_cells = c("auto", "none", "grouping",
  "feature", "milestone", "pseudotime"),
  dimred = ifelse(dynwrap::is_wrapper_with_dimred(trajectory), NA,
  ifelse(length(trajectory$cell_ids) > 500, dimred_pca, dimred_mds)),
  plot_trajectory = dynwrap::is_wrapper_with_trajectory(trajectory) &&
  !plot_milestone_network, plot_milestone_network = FALSE,
  label_milestones = dynwrap::is_wrapper_with_milestone_labelling(trajectory),
  alpha_cells = 1, size_trajectory = 1, grouping = NULL,
  groups = NULL, feature_oi = NULL, color_milestones = c("auto",
  "given", "cubeHelix", "Set3", "rainbow"), milestones = NULL,
  milestone_percentages = NULL, pseudotime = NULL,
  expression_source = "expression", color_density = c("none",
  "grouping", "feature"), padding = 0.1, nbins = 1000, bw = 0.2,
  density_cutoff = 0.3, density_cutoff_label = density_cutoff/10,
  waypoints = dynwrap::select_waypoints(trajectory),
  trajectory_projection_sd = sum(trajectory$milestone_network$length) *
  0.05, color_trajectory = "none")

Arguments

trajectory	The trajectory
color_cells	How to color the cells
dimred	The dimensionality reduction matrix (with cell_ids as rownames) or function which will run the dimensionality reduction
plot_trajectory	Whether to plot the projected trajectory on the dimensionality reduction
plot_milestone_network	Whether to plot the projected milestone network on the dimensionality reduction
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
alpha_cells	The alpha of the cells
size_trajectory	The size of the trajectory segments
grouping	The grouping of the cells
groups	Tibble containing information of the cell groups
feature_oi	feature to plot expression
color_milestones	How to color the cells
milestones	Tibble containing the `milestone_id` and a `color` for each milestone
milestone_percentages	The milestone percentages
pseudotime	The pseudotime
expression_source	Source of the expression
color_density	How to color density, can be "none", "grouping", or "feature"
padding	The padding in the edges to the plot, relative to the size of the plot
nbins	Number of bins for calculating the density
bw	Bandwidth, relative to the size of the plot
density_cutoff	Cutoff for density, the lower the larger the areas
density_cutoff_label	Cutoff for density for labelling, the lower the further way from cells
waypoints	The waypoints to use for projecting, as generated by [dynwrap::select_waypoints()]
trajectory_projection_sd	The standard deviation of the gaussian kernel to be used for projecting the trajectory. This is in the order of maginature as the lengths of the milestone_network. The lower, the more closely the trajectory will follow the cells
color_trajectory	How to color the trajectory, can be "nearest" for coloring to nearest cell, or "none"

Examples

data(example_bifurcating)
plot_dimred(example_bifurcating)
#> Coloring by milestone
#> Using milestone_percentages from trajectory
plot_dimred(example_bifurcating, dimred = dyndimred::dimred_umap)
#> Coloring by milestone
#> Using milestone_percentages from trajectory
dimred <- dyndimred::dimred_dm_destiny(example_bifurcating$expression)
plot_dimred(example_bifurcating, dimred = dimred)
#> Coloring by milestone
#> Using milestone_percentages from trajectory
plot_dimred(example_bifurcating, color_cells = "pseudotime")
#> Pseudotime not provided, will calculate pseudotime from root milestone
#> root cell or milestone not provided, trying first outgoing milestone_id
#> Using 'M1' as root
plot_dimred(
  example_bifurcating,
  color_density = "grouping",
  grouping = dynwrap::group_onto_nearest_milestones(example_bifurcating)
)
#> Coloring by grouping