Step 2: latent_to_gene

usage: gsmap run_latent_to_gene [-h] --workdir WORKDIR --sample_name
                                SAMPLE_NAME
                                [--input_hdf5_path INPUT_HDF5_PATH]
                                [--no_expression_fraction]
                                [--latent_representation LATENT_REPRESENTATION]
                                [--num_neighbour NUM_NEIGHBOUR]
                                [--num_neighbour_spatial NUM_NEIGHBOUR_SPATIAL]
                                [--homolog_file HOMOLOG_FILE]
                                [--gM_slices GM_SLICES]
                                [--annotation ANNOTATION]

Named Arguments

--workdir

Path to the working directory.

--sample_name

Name of the sample.

--input_hdf5_path

Path to the input HDF5 file with latent representations, if –latent_representation is specified.

--no_expression_fraction

Skip expression fraction filtering.

Default: False

--latent_representation

Type of latent representation. This should exist in the h5ad obsm.

--num_neighbour

Number of neighbors.

Default: 21

--num_neighbour_spatial

Number of spatial neighbors.

Default: 101

--homolog_file

Path to homologous gene conversion file (optional).

--gM_slices

Path to the slice mean file (optional).

--annotation

Name of the annotation in adata.obs to use (optional).