Plot the trajectory on dimensionality reduction
plot_dimred(traj, color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"), dimred = ifelse(dynwrap::is_wrapper_with_dimred(traj), NA, ifelse(length(traj$cell_ids) > 500, dimred_pca, dimred_mds)), plot_trajectory = dynwrap::is_wrapper_with_trajectory(traj) && !plot_milestone_network, plot_milestone_network = FALSE, label_milestones = dynwrap::is_wrapper_with_milestone_labelling(traj), grouping = NULL, groups = NULL, feature_oi = NULL, color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"), milestones = NULL, milestone_percentages = NULL, pseudotime = NULL, expression_source = "expression", color_density = c("none", "grouping", "feature"), padding = 0.1, nbins = 1000, bw = 0.2, density_cutoff = 0.3, density_cutoff_label = density_cutoff/10, trajectory_projection_sd = sum(traj$milestone_network$length) * 0.05, n_arrows = 10)
| traj | 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 |
| 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 |
| 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 |
| n_arrows | Number of arrows to add to trajectory projection |