compileCellDataSet.Rd
Takes the count matrix of your spata-object and creates a cell_data_set-object with it. See details for more information on how to use the arguments.
compileCellDataSet( object, preprocess_method = "PCA", reduction_method = c("PCA", "UMAP"), cluster_method = "leiden", estimate_size_factors_args = list(), preprocess_cds_args = list(), reduce_dimension_args = list(), cluster_cells_args = list(), learn_graph_args = list(), order_cells_args = list(), save_cds_file = NULL, verbose = TRUE )
object | A valid spata-object. |
---|---|
preprocess_method | Monocle3 - description: A string specifying the initial dimension method to use, currently either PCA or LSI. For LSI (latent semantic indexing), it converts the (sparse) expression matrix into tf-idf matrix and then performs SVD to decompose the gene expression / cells into certain modules / topics. Default is "PCA". |
reduction_method | Monocle3 - description: A character string specifying the algorithm to use for dimensionality reduction. Currently "UMAP", "tSNE", "PCA" and "LSI" are supported. |
cluster_method | Monocle3 - description: String indicating the clustering method to use. Options are "louvain" or "leiden". Default is "leiden". Resolution parameter is ignored if set to "louvain". |
estimate_size_factors_args | A list of arguments given to |
preprocess_cds_args | A list of arguments given to |
reduce_dimension_args | A list of arguments given to |
cluster_cells_args | A list of arguments given to |
learn_graph_args | A list of arguments given to |
order_cells_args | A list of arguments given to |
save_cds_file | Character value or NULL. A file-directory (that does not already exists) under which created cell_data_set-object is saved. Should end with '.RDS'. |
verbose | Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
A monocle3::cell_data_set object.
compileCellDataSet()
is a convenient wrapper around all pre processing functions
monocle3 provides to handle it's core object - the cell_data_set - after it's initiation. Apart from unique
arguments this function has two argument families, denoted with _method
and _args
.
Handling _method
-arguments:
Monocle3 allows to use different methods for dimensional-reduction or clustering which depend
on each other. These arguments take a character vector of all valid inputs. compileCellDataSet()
iterates
over all valid combinations and returns the cell_data_set with the computed information inside.
Handling _args
-arguments.
These arguments take named lists of arguments that are given to the respective function. The _method
-arguments
as well as the argument cds
are automatically defined and must not be included in the given lists!!! Empty lists - the default -
result in running the function with it's default parameters.
The spata-objects feature data (@fdata) is passed to the cell_data_set for it's slot cell_meta_data