`plot_dimred.Rd`

Plot a trajectory on dimensionality reduction

plot_dimred(trajectory, color_cells = c("auto", "none", "grouping", "feature", "milestone", "pseudotime"), dimred = ifelse(dynwrap::is_wrapper_with_dimred(trajectory), NA, ifelse(length(trajectory$cell_ids) > 500, dimred_pca, dimred_mds)), plot_trajectory = dynwrap::is_wrapper_with_trajectory(trajectory) && !plot_milestone_network, plot_milestone_network = FALSE, label_milestones = dynwrap::is_wrapper_with_milestone_labelling(trajectory), alpha_cells = 1, size_trajectory = 1, grouping = NULL, groups = NULL, feature_oi = NULL, color_milestones = c("auto", "given", "cubeHelix", "Set3", "rainbow"), milestones = NULL, milestone_percentages = NULL, pseudotime = NULL, expression_source = "expression", color_density = c("none", "grouping", "feature"), padding = 0.1, nbins = 1000, bw = 0.2, density_cutoff = 0.3, density_cutoff_label = density_cutoff/10, waypoints = dynwrap::select_waypoints(trajectory), trajectory_projection_sd = sum(trajectory$milestone_network$length) * 0.05, color_trajectory = "none")

trajectory | The trajectory |
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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 |

alpha_cells | The alpha of the cells |

size_trajectory | The size of the trajectory segments |

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 |

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 maginature 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" |

#>#>#>#>dimred <- dyndimred::dimred_dm_destiny(example_bifurcating$expression) plot_dimred(example_bifurcating, dimred = dimred)#>#>#>#>#>plot_dimred( example_bifurcating, color_density = "grouping", grouping = dynwrap::group_onto_nearest_milestones(example_bifurcating) )#>