SCORPIUS-package | R Documentation |
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). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/079509")} (PDF).
## 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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