# Visualising Single-Cell Trajectories

## Documentation for package ‘dynplot’ version 1.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_cell_coloring | Add colouring to a set of cells.
add_density_coloring | Color cells using a background density
add_milestone_coloring | Add colouring to a set of milestones.
dynplot | dynplot: Plotting Single-Cell Trajectories
empty_plot | Create an empty plot for spacing
example_bifurcating | An example bifurcating dataset
example_disconnected | An example disconnected dataset
example_linear | An example linear dataset
example_tree | An example tree dataset
get_milestone_palette_names | Get the names of valid color palettes
linearise_cells | Prepare a trajectory for linearised visualisation.
milestone_palette | Get the names of valid color palettes
plot_default | Plot a trajectory as a graph
plot_dendro | Plot a trajectory as a dendrogram
plot_dimred | Plot a trajectory in a (given) dimensionality reduction
plot_graph | Plot a trajectory as a graph
plot_heatmap | Plot expression data along a trajectory
plot_linearised_comparison | Compare two trajectories as a pseudotime scatterplot
plot_onedim | Plot a trajectory as a one-dimensional set of connected segments
plot_strip | Plot strip
plot_topology | Plot the topology of a trajectory
project_waypoints_coloured | Project the waypoints
theme_clean | We like our plots clean
theme_graph | We like our plots clean