nbnode.apply package

Submodules

nbnode.apply.count_celltree_df module

nbnode.apply.count_celltree_df.count_celltree_df(celltree_gated: NBNode) → DataFrame

Count the number of rows in node.data (per node) grouped by “sample_name” and concat them into a dataframe

Parameters:

celltree_gated (NBNode) – A gated celltree, e.g. as result from gate_csv()

Returns:

pd.DataFrame with

rows: Samples columns: Nodes values: Counts index: Sample identifier

Examples

>>> import os
>>> from nbnode.apply.gate_csv import gate_csv
>>> rescaled_data_dir = os.path.join(
...    "example_data", "asinh.align_manual.CD3_Gate"
...    )
>>> if not os.path.exists(rescaled_data_dir):
...     raise FileNotFoundError(
...         rescaled_data_dir,
...         " has not been found, did you run tests/examples/e01_download.sh?",
...         )
>>> rescaled_data_dir_files = [
...     os.path.join(rescaled_data_dir, file_x)
...     for file_x in os.listdir(rescaled_data_dir)
... ]
>>> print(rescaled_data_dir_files)
>>> a = gate_csv(csv=rescaled_data_dir_files[0])
>>> b = gate_csv(csv=rescaled_data_dir_files[0:3])
>>> from nbnode.apply.count_celltree import count_celltree_df
>>> print(count_celltree_df(a))
>>> print(count_celltree_df(b))

nbnode.apply.gate_csv module

nbnode.apply.gate_csv.gate_csv(csv: str | List[str], celltree='default', new_colnames=['FS', 'FS.0', 'SS', 'CD45RA', 'CCR7', 'CD28', 'PD1', 'CD27', 'CD4', 'CD8', 'CD3', 'CD57', 'CD45'], verbose=True)

_summary_

Parameters:

• csv (Union[str, List[str]]) – Path to a single .csv file or a list of .csv files

• celltree (str, optional) – _description_. Defaults to “default”.

• new_colnames (List[str]) – vector of new colnames for the csvs. Usually used to make the colnames of the csvs matching to the celltree.

• verbose (bool, optional) – _description_. Defaults to True.

Returns:

_description_

Return type:

_type_

Examples

>>> rescaled_data_dir = os.path.join(
...     "example_data", "asinh.align_manual.CD3_Gate")
>>> if not os.path.exists(rescaled_data_dir):
...     raise FileNotFoundError(
...         rescaled_data_dir,
...         " has not been found, did you run tests/examples/e01_download.sh?",
...         )
>>> rescaled_data_dir_files = [os.path.join(rescaled_data_dir, file_x)
... for file_x in os.listdir(rescaled_data_dir)]
>>> print(rescaled_data_dir_files)
>>> gate_csv(csv=rescaled_data_dir_files[0])
>>> gate_csv(csv=rescaled_data_dir_files[0:3])

nbnode.apply.gate_pointcloud module

Module contents