CellRouter

Will generate a trajectory using CellRouter.

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

ti_cellrouter(ndim_pca = 20L, ndim_tsne = 11L, max_iter = 1000L,
  cluster_method = "graph.clustering", k_clustering = 20L,
  ndim_pca_clustering = 20L, k_knn = 10L, ndim_pca_knn = 20L,
  sim_type = "jaccard", distance_method_paths = "graph",
  ranks = "rank", num_cells = 3L, neighs = 3L, perplexity = 30L)

Arguments

ndim_pca

Number of principal components to compute. Domain: U(2, 100). Default: 20. Format: integer.
ndim_tsne

Number of tsne dimensions to compute. Domain: U(2, 100). Default: 11. Format: integer.
max_iter

Maximal number of tsne iterations. Domain: e^U(4.61, 11.51). Default: 1000. Format: integer.
cluster_method

Method to use for clustering. Domain: graph.clustering, model.clustering. Default: graph.clustering. Format: character.
k_clustering

Number of nearest neighbors to build a k-nearest neighbors graph for clustering. Domain: U(2, 1000). Default: 20. Format: integer.
ndim_pca_clustering

Number of PCA dimensions used for k-nearest neighbors graph for clustering. Domain: U(2, 100). Default: 20. Format: integer.
k_knn

Number of nearest neighbors to build a k-nearest neighbors graph for knn. Domain: e^U(0.69, 6.91). Default: 10. Format: integer.
ndim_pca_knn

Number of PCA dimensions used for knn. Domain: U(2, 100). Default: 20. Format: integer.
sim_type

Similarity type for knn. Domain: jaccard. Default: jaccard. Format: character.
distance_method_paths

Distance method for paths. Domain: euclidean, maximum, manhattan, canberra, binary, graph. Default: graph. Format: character.
ranks

How to rank the paths. Domain: path_cost, path_flow, rank, length. Default: rank. Format: character.
num_cells

Trajectories should contain at least num.cells. Domain: U(3, 100). Default: 3. Format: integer.
neighs

The size of the neighborhood in kNN graph used to smoothen kinetic profiles. Domain: U(2, 100). Default: 3. Format: integer.
perplexity

Perplexity parameter for tsne. Domain: U(5, 100). Default: 30. Format: numeric.

Value

A TI method wrapper to be used together with infer_trajectory

References

Lummertz da Rocha, E., Rowe, R.G., Lundin, V., Malleshaiah, M., Jha, D.K., Rambo, C.R., Li, H., North, T.E., Collins, J.J., Daley, G.Q., 2018. Reconstruction of complex single-cell trajectories using CellRouter. Nature Communications 9.