SCORPIUS

Will generate a trajectory using SCORPIUS.

This method was wrapped inside a container. The original code of this method is available here.

ti_scorpius(distance_method = "spearman", ndim = 3L, k = 4L,
  thresh = 0.001, maxit = 10L, stretch = 0,
  smoother = "smooth_spline", sparse = TRUE)

Arguments

distance_method

A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "kendall", or "spearman". Domain: spearman, pearson, kendall. Default: spearman. Format: character.
ndim

The number of dimensions in the new space. Domain: U(2, 20). Default: 3. Format: integer.
k

The number of clusters to cluster the data into. Domain: U(1, 20). Default: 4. Format: integer.
thresh

principal_curve parameter; convergence threshhold on shortest distances to the curve. Domain: e^U(-11.51, 11.51). Default: 0.001. Format: numeric.
maxit

principal_curve parameter; maximum number of iterations. Domain: U(0, 50). Default: 10. Format: integer.
stretch

principal_curve parameter; a factor by which the curve can be extrapolated when points are projected. Domain: U(0, 5). Default: 0. Format: numeric.
smoother

principal_curve parameter; choice of smoother. Domain: smooth_spline, lowess, periodic_lowess. Default: smooth_spline. Format: character.
sparse

Whether or not to use sparse MDS dimensionality reduction, for datasets with large amounts of cells. Default: TRUE. Format: logical.

Value

A TI method wrapper to be used together with infer_trajectory

References

Cannoodt, R., Saelens, W., Sichien, D., Tavernier, S., Janssens, S., Guilliams, M., Lambrecht, B.N., De Preter, K., Saeys, Y., 2016. SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development.