Command-Line Interface

Cytomulate can be accessed through the commandline through the OS/shell of your choice. Here is the detailed documentation of the CLI along with its implementation.

main.py

The Command-Line Interface (CLI) of Cytomulate

For convenience, users can access cytomulate without the need of writing a script. Consistent with python CLI syntax, this __main__.py can be accessed through python -m cytomulate. The CLI has the advantages of convenience while also supporting most functionalities of the packages.

Example:

Check version:

python -m cytomulate --version

Get help:

python -m cytomulate -h

Advantage:

Shell-scripting friendly
Easy-to-use
No python knowledge required

Drawbacks:

Not as configurable as a python program
Top level functionality and integration only (i.e. No partial package usage)

Arguments and Flags

CLI Parser Documentation

cytomulate: CyTOF Simulation

usage: CLI Parser Documentation [-h] [--version] [--creation]
                                [--n_cells N_CELLS] [--n_batches N_BATCHES]
                                [--n_types N_TYPES] [--n_markers N_MARKERS]
                                [--n_trees N_TREES] [--emulation]
                                [--exprs EXPRS] [--cell_types CELL_TYPES]
                                [--exprs_colnames] [--cell_types_colnames]
                                [--exprs_delim EXPRS_DELIM]
                                [--cell_types_delim CELL_TYPES_DELIM]
                                [--trajectory] [--temporal_effect]
                                [--temporal_effect_var TEMPORAL_EFFECT_VAR]
                                [--batch_effect]
                                [--batch_effect_var BATCH_EFFECT_VAR]
                                [-o OUT_DIR] [--make_new_dir]

-h, --help: show this help message and exit

--version: show program’s version number and exit

--creation: Creation mode of Cytomulate.

--n_cells <n_cells>: The number of cells to simulate

--n_batches <n_batches>: The number of batches

--n_types <n_types>: The number of cell types to simulate.

--n_markers <n_markers>: The number of markers to simulate.

--n_trees <n_trees>: The number of differentiation trees to simulate.

--emulation: Creation mode of Cytomulate.

--exprs <exprs>: The path to existing expression matrix.

--cell_types <cell_types>: The path to existing cell types.

--exprs_colnames: Whether the first row of the existing expression matrix is column names.

--cell_types_colnames: Whether the first row of the existing cell types is column names.

--exprs_delim <exprs_delim>: The delimiter of existing expression matrix.

--cell_types_delim <cell_types_delim>: The delimiter of existing cell types.

--trajectory: Add cell differentiation trajectory.

--temporal_effect: Add temporal effect to the dataset. Only the Brownian Bridge method is supported.

--temporal_effect_var <temporal_effect_var>: Add cell differentiation trajectory.

--batch_effect: Add batch effect to the dataset.

--batch_effect_var <batch_effect_var>: Add cell differentiation trajectory.

-o <out_dir>, --out_dir <out_dir>: Directory to save simulation data files

--make_new_dir: Directory to save simulation data files

Command-Line Interface

__main__.py

Arguments and Flags

CLI Parser Documentation

main.py