Description Dimensionality Reduction functions Trajectory Inference functions Visualisation functions Datasets References Examples
SCORPIUS orders single cells with regard to an implicit timeline, such as cellular development or progression over time.
reduce_dimensionality
infer_trajectory
, infer_initial_trajectory
, reverse_trajectory
, gene_importances
, extract_modules
draw_trajectory_plot
, draw_trajectory_heatmap
generate_dataset
, ginhoux
Cannoodt R. et al., SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development, bioRxiv (Oct., 2016). doi: 10.1101/079509 (PDF).
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Load dataset from Schlitzer et al., 2015
data("ginhoux")
## Reduce dimensionality and infer trajectory with SCORPIUS
space <- reduce_dimensionality(ginhoux$expression, "spearman")
traj <- infer_trajectory(space)
## Visualise
draw_trajectory_plot(
space,
path = traj$path,
progression_group = ginhoux$sample_info$group_name
)
|
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