Will generate a trajectory using Mpath.
This method was wrapped inside a container. The original code of this method is available here.
ti_mpath(distMethod = "euclidean", method = "kmeans", numcluster = 11L, numcluster_null = TRUE, diversity_cut = 0.6, size_cut = 0.05, run_environment = NULL)
| distMethod | discrete; The method for calculating dissimilarity between
cells. distMethod can be one of "pearson", "kendall", "spearman" or
"euclidean". Default is "euclidean". (default: |
|---|---|
| method | discrete; Method for distinguishing landmark clusters from
non-landmark clusters.method can be "kmeans" or "diversity" or "size" or
"diversity_size". When method="diversity", numlm needs to be specified. Default
is "diversity_size". (default: |
| numcluster | integer; Number of initial clusters (default: |
| numcluster_null | logical; If TRUE, will automatically select the number of clusters |
| diversity_cut | numeric; The cutoff value of diversity for differentiating
landmark clusters from non-landmark clusters. The diversity of a landmark
cluster must be below this cutoff. (default: |
| size_cut | numeric; The cutoff value of size i.e. number of cells for
differentiating landmark clusters from non-landmark clusters. The number of
cells in a landmark cluster must be greater than this cutoff. (default: |
| run_environment | In which environment to run the method, can be |
A TI method wrapper to be used together with
infer_trajectory
Chen, J., Schlitzer, A., Chakarov, S., Ginhoux, F., Poidinger, M., 2016. Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development. Nature Communications 7, 11988.