add_density_coloring.RdColor cells using a background density
add_density_coloring(cell_positions, color_density = c("none", "grouping", "feature"), trajectory, 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)
| cell_positions | The positions of the cells in 2D |
|---|---|
| color_density | How to color density, can be "none", "grouping", or "feature" |
| trajectory | 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 |