stereo.io.read_gef#
- stereo.io.read_gef(file_path, bin_type='bins', bin_size=100, is_sparse=True, gene_list=None, region=None, gene_name_index=False)[source]#
Read the GEF (.h5) file, and generate the StereoExpData object.
- Parameters:
file_path (
str
) – the path to input file.bin_type (
str
) – the bin type includes'bins'
or'cell_bins'
.bin_size (
int
) – the size of bin to merge, which only takes effect when thebin_type
is set as'bins'
.is_sparse (
bool
) – the matrix is sparse matrix, ifTrue
, otherwisenp.ndarray
.gene_list (
Optional
[list
]) – select targeted data based on the gene list.region (
Optional
[list
]) – restrict data to the region condition, like [minX, maxX, minY, maxY].gene_name_index (
Optional
[bool
]) –True
to set gene name as index if the version of gef file is 4 or greater, otherwise to set gene id, if the version is 3 or less,gene_name_index
would be forced toTrue
because there is no gene id in this case.
- Return type:
An object of StereoExpData.