stereo.core.StereoExpData

class stereo.core.StereoExpData(file_path=None, file_format=None, bin_type=None, bin_size=100, exp_matrix=None, genes=None, cells=None, position=None, position_z=None, output=None, partitions=1, offset_x=None, offset_y=None, attr=None, merged=False)

__init__(file_path=None, file_format=None, bin_type=None, bin_size=100, exp_matrix=None, genes=None, cells=None, position=None, position_z=None, output=None, partitions=1, offset_x=None, offset_y=None, attr=None, merged=False)

The core data object is designed for expression matrix of spatial omics, which can be set corresponding properties directly to initialize the data.

Parameters:

• file_path (Optional[str]) – the path to input file of expression matrix.

• file_format (Optional[str]) – the format of input file.

• bin_type (Optional[str]) – the type of bin, if the file format is Stereo-seq file including 'bins' or 'cell_bins'.

• bin_size (Optional[int]) – the size of the bin to merge, when bin_type is 'bins'.

• exp_matrix (Union[ndarray, spmatrix, None]) – the expression matrix.

• genes (Union[ndarray, Gene, None]) – the gene object which contains information of gene level.

• cells (Union[ndarray, Cell, None]) – the cell object which contains information of cell level.

• position (Optional[ndarray]) – spatial location information.

• output (Optional[str]) – the path to output file.

• partitions (Optional[int]) – the number of multi-process cores, used when processing files in parallel.

• offset_x (Optional[str]) – the x value of the offset .

• offset_y (Optional[str]) – the y value of the offset .

• attr (Optional[dict]) – attribute information from GEF file.

Methods

__init__([file_path, file_format, bin_type, ...])	The core data object is designed for expression matrix of spatial omics, which can be set corresponding properties directly to initialize the data.
array2sparse()	Transform expression matrix to sparse matrix if it is ndarray.
bin_type_check(bin_type)	Check whether the bin type is from specific options.
check()	Check whether the parameters meet the requirement.
file_check(file)	Check whether the file exists.
format_check(f_format)	Check whether the file format is in specific range.
get_index(data, names)
get_sn_from_path(file_path)	Get the SN information of input file.
issparse()	Check whether the matrix is sparse matrix type.
output_check(path)	Check whether the output directory exists.
reset_position()
sparse2array()	Transform expression matrix to array if it is parse matrix.
sub_by_index([cell_index, gene_index])	Get data subset by indexl list of cells or genes.
sub_by_name([cell_name, gene_name])	Get data subset by name list of cells or genes.
sub_exp_matrix_by_name([cell_name, ...])	rtype: Union[ndarray, spmatrix]
to_ann_based()
to_df()	Transform StereoExpData object to pd.DataFrame.
write(filename[, to_anndata])

Attributes

attr	Get the attribute information.
bin_size	Get the bin size.
bin_type	Get the bin type.
cell_borders	Get the cell borders.
cell_names	Get the cell names.
cells	Get the cell object.
cells_matrix	Get the cells matrix.
cells_pairwise	Get the cells pairwise.
exp_matrix	Get the expression matrix.
file	Get the file property.
file_format	Get the file format.
gene_names	Get the gene names.
genes	Get the gene object.
genes_matrix	Get the genes matrix.
genes_pairwise	Get the genes pairwise.
merged	Get the flag whether merged.
offset_x	Get the x value of the offset.
offset_y	Get the y value of the offset.
output	Get the path to ouput file.
partitions	Get the partitions property.
plt	Call the visualization module.
position	Get the information of spatial location.
position_min
position_offset	Get the offset of position in gef.
position_z
raw
raw_position
resolution
shape	Get the shape of expression matrix.
sn	Get the sample name.
tl	call StPipeline method.