arcfish.pp.FOF_CT_Loader

class arcfish.pp.FOF_CT_Loader(path: str | list | dict, nm_ratio: dict | None = None, var_cols_add: list | None = None, obs_cols_add: list | None = None, **kwargs)

Read in FOF_CT file(s).

For FOF_CT-core files, call create_adata() to create an AnnData. The x, y, and z coordinates of each chromatin trace are stored as layers. If multiple file paths are passed in, merge traces from all the files.

When having multiple files, will add a prefix to Trace_ID to make it unique. If path is a list, will add a single number prefix to Trace_ID. If path is a dictionary, prepend the dictionary key to Trace_ID.

For other FOF_CT files, call read_data() to read in the data field as a dataframe. The only required argument is path, all other arguments passed to the constructor will be ignored.

Parameters:

• path (str | list | dict) – The path of the FOF_CT file. Can be a list or a dictionary specifying multiple files.

• nm_ratio (dict | None, optional) – The conversion factor to convert raw coordinate to physical coordinate in nm. No conversion if None, by default None.

• var_cols_add (list | None, optional) – Additional columns added to var field in the AnnData object, by default None.

• obs_cols_add (list | None, optional) – Additional columns added to obs field in the AnnData object, by default None.

• kwargs (dict) – Additional keyword arguments passed to anndata.AnnData constructor.

Raises:

ValueError – If path is not a string, a list, or a dictionary.

__init__(path: str | list | dict, nm_ratio: dict | None = None, var_cols_add: list | None = None, obs_cols_add: list | None = None, **kwargs)

Methods

__init__(path[, nm_ratio, var_cols_add, ...])
create_adata(chr_id)	Create an anndata.AnnData object from a single or multiple FOF_CT-core files.
read_data()	Read the data field of the file(s).

Attributes

chr_ids	Available chromosomes in FOF_CT-core.
info	If path is a single file name, returns a dictionary of the header information.
nm_ratio	Conversion factor to convert voxel coordinate to actual physical coordinate.
path	Path of input files.

property path: str | list | dict

Path of input files.

Type:

str|list|dict

property nm_ratio: dict | None

Conversion factor to convert voxel coordinate to actual physical coordinate.

Type:

dict|None

property info: list | dict

If path is a single file name, returns a dictionary of the header information. If path is a list, returns a list of information dictionaries. If path is a dictionary, returns a dictionary of information dictionaries.

Type:

list|dict

property chr_ids: ndarray

Available chromosomes in FOF_CT-core.

Type:

np.ndarray

read_data() → DataFrame | list | dict

Read the data field of the file(s).

Returns:

A single dataframe, a list of dataframes, or a dictionary of dataframes, depending on the type of path.

Return type:

pd.DataFrame|list|dict

create_adata(chr_id: str) → AnnData

Create an anndata.AnnData object from a single or multiple FOF_CT-core files. The output is for a single chromosome instead of all chromosomes imaged.

Parameters:

chr_id (str) – Chromosome ID used to filter Chrom column.

Returns:

A n by p AnnData object, where n is the number of traces, and p is the number of locus on the chromosome. var field includes Chrom_Start, Chrom_End, and any additional columns specified by var_cols_add. obs field includes columns specified by obs_cols_add. The converted 3D coordinates are stored in layers with names X, Y, and Z.

Return type:

AnnData