Plot onedim
plot_onedim(traj, color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"), milestone_network = traj$milestone_network, progressions = traj$progressions, grouping = NULL, groups = NULL, feature_oi = NULL, pseudotime = NULL, expression_source = "expression", color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"), milestones = NULL, milestone_percentages = NULL, orientation = 1, margin = 0.05, linearised = linearise_cells(milestone_network, progressions, margin, one_edge = TRUE), quasirandom_width = 0.2, plot_cells = TRUE, label_milestones = dynwrap::is_wrapper_with_milestone_labelling(traj))
| traj | The trajectory |
|---|---|
| color_cells | How to color the cells |
| milestone_network | Optional, the milestone network |
| progressions | The progressions used to put the cells on the graph |
| grouping | The grouping of the cells |
| groups | Tibble containing information of the cell groups |
| feature_oi | feature to plot expression |
| pseudotime | The pseudotime |
| expression_source | Source of the feature expression, defaults to `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 |
| orientation | Whether to plot the connections in the top (1) or bottom (-1) |
| margin | The margin to add |
| linearised | The linearised milestone network and progressions |
| quasirandom_width | The width of the quasirandom cell spreading |
| plot_cells | Whether to plot the cells |
| 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 |