plot_dimred: Plot a trajectory in a (given) dimensionality reduction

Description Usage Arguments Value Examples

Description

Plot a trajectory in a (given) dimensionality reduction

Usage

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plot_dimred(
  trajectory,
  color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"),
  dimred = ifelse(dynwrap::is_wrapper_with_dimred(trajectory), NA,
    dyndimred::dimred_landmark_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_cells = 2.5,
  border_radius_percentage = 0.1,
  size_milestones = 6,
  size_transitions = 2,
  hex_cells = ifelse(length(trajectory$cell_ids) > 10000, 100, FALSE),
  grouping = NULL,
  groups = NULL,
  feature_oi = NULL,
  color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"),
  milestones = NULL,
  milestone_percentages = NULL,
  pseudotime = NULL,
  expression_source = "expression",
  arrow = grid::arrow(type = "closed", length = unit(0.1, "inches")),
  color_density = c("none", "grouping", "feature"),
  padding = 0.1,
  nbins = 1000,
  bw = 0.2,
  density_cutoff = 0.3,
  density_cutoff_label = density_cutoff/10,
  waypoints = dynwrap::select_waypoints(trajectory),
  trajectory_projection_sd = sum(trajectory$milestone_network$length) * 0.05,
  color_trajectory = "none"
)

Arguments

trajectory

The trajectory

color_cells

How to color the cells

dimred

Can be

  • A function which will perform the dimensionality reduction, see dyndimred::list_dimred_methods()

  • A matrix with the dimensionality reduction, with cells in rows and dimensions (comp_1, comp_2, ...) in columns

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_cells

The size of the cells

border_radius_percentage

The fraction of the radius that is used for the border

size_milestones

The size of the milestones

size_transitions

The size of the trajectory segments

hex_cells

The number of hexes to use, to avoid overplotting points. Default is FALSE if number of cells <= 10000.

grouping

The grouping of the cells

groups

Tibble containing information of the cell groups

feature_oi

feature to plot expression

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

pseudotime

The pseudotime

expression_source

Source of the expression

arrow

The type and size of arrow in case of directed trajectories. Set to NULL to remove arrow altogether.

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 magnitude 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"

Value

A dimensionality reduction ggplot of the data.

Examples

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data(example_bifurcating)
plot_dimred(example_bifurcating)


# plotting with umap
if (requireNamespace("uwot", quietly = TRUE)) {
  plot_dimred(example_bifurcating, dimred = dyndimred::dimred_umap)
}

# using a custom dimred
dimred <- dyndimred::dimred_mds(example_bifurcating$expression)
plot_dimred(example_bifurcating, dimred = dimred)

# coloring cells by pseudotime
plot_dimred(example_bifurcating, color_cells = "pseudotime")

# coloring cells by cluster
plot_dimred(
  example_bifurcating,
  color_density = "grouping",
  grouping = dynwrap::group_onto_nearest_milestones(example_bifurcating)
)

dynverse/dynplot documentation built on June 18, 2021, 12:10 p.m.