Color cells using a background density

add_density_coloring(cell_positions, color_density = c("none",
  "grouping", "feature"), traj, grouping = NULL, groups = NULL,
  feature_oi = NULL, expression_source = "expression", padding = 0.1,
  nbins = 1000, bw = 0.2, density_cutoff = 0.3,
  density_cutoff_label = density_cutoff/10)

Arguments

cell_positions

The positions of the cells in 2D

color_density

How to color density, can be "none", "grouping", or "feature"

traj

The trajectory

grouping

The grouping of the cells

groups

Tibble containing information of the cell groups

feature_oi

feature to plot expression

expression_source

Source of the feature expression, defaults to `expression`

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