CalculateScaffoldTree: Calculate Scaffold tree
In soedinglab/merlot: MERLoT

creates the scaffold tree from the expression matrix in the Dataset object.

CalculateScaffoldTree(CellCoordinates, NEndpoints = NULL,
  BranchMinLength = -1, BranchMinLengthSensitive = -1, reduced = 0,
  python_location = "python3", docker = NULL, tmp_dir = NA,
  rm_tmp = TRUE, random_seed = 42)

`CellCoordinates`	file containing coordinates from the low dimensional manifold (e.g: first 3 diffusion components from a diffusion map)
`NEndpoints`	Users can specify how many endpoints they want the algorithm to find. In case this variable is not defined all branches producing branches longer than sqrt(N/2) will be added to the tree structure
`BranchMinLength`	Minimum number of nodes a branch has to contain in order to be included in the 3 structure. By default this value is set to sqrt(N/2) with N being the total number of cells in the dataset.
`BranchMinLengthSensitive`	Minimum length for a branch to be included in the tree. It reconstructs the topology of the tree and maps cells to the potential new branch to decide if the branch will be added or not. Suggested value: sqrt(N) with N being the number of cells in the dataset
`reduced`	The number of clusters to group cells in. If set to 0, no clustering will be performed and the scaffold tree will be calculated on all cells (default).
`python_location`	The url to the python3 executable binary. In case it is not specified a default call to python3 will be used.
`docker`	The name of the docker container that accompanies MERLoT (alternative to using a local python installation).
`tmp_dir`	The name of the directory where temporary files generated by the scaffold tree calculation will be saved. Will be in the system temporary folder by default.
`rm_tmp`	A flag that controls whether the temporary files generated by the scaffold tree calculation should be removed or not.
`random_seed`	Random seed to be passed on to Python to ensure reproducibility.