GeneExpressionAPI#

class brainrender.atlas_specific.allen_brain_atlas.gene_expression.api.GeneExpressionAPI[source]#

Bases: object

Client for querying and downloading Allen Brain Atlas gene expression data.

Methods

download_gene_data(**kwargs)

get_all_genes(**kwargs)

get_gene_data(gene, exp_id[, use_cache, metric])

Load gene expression data for a given gene and experiment.

get_gene_experiments(**kwargs)

get_gene_id_by_name(gene_name)

Return the Allen gene ID for a given gene symbol.

get_gene_symbol_by_id(gene_id)

Return the gene symbol for a given Allen gene ID.

griddata_to_volume(griddata[, min_quantile, ...])

Convert a 3D gene expression array to a Volume actor.

Attributes

all_genes_url

download_url

gene_experiments_url

gene_expression_cache

gene_name

grid_size

voxel_size

get_gene_data(gene, exp_id, use_cache=True, metric='energy')[source]#

Load gene expression data for a given gene and experiment.

Parameters:

  • gene (str) – Gene symbol.

  • exp_id (int) – Experiment ID.

  • use_cache (bool) – If True, load from cache if available. Default True.

  • metric (str) – Expression metric to load. Default "energy".

Returns:

Gene expression data, or None if no data is available for the requested metric.

Return type:

numpy.ndarray or None

Raises:

ValueError – If data could not be cached after downloading.

get_gene_id_by_name(gene_name)[source]#

Return the Allen gene ID for a given gene symbol.

Parameters:

gene_name (str) – Gene symbol.

Returns:

Gene ID, or None if the gene is not found.

Return type:

int or None

get_gene_symbol_by_id(gene_id)[source]#

Return the gene symbol for a given Allen gene ID.

Parameters:

gene_id (int | str) – Allen gene ID.

Return type:

str

griddata_to_volume(griddata, min_quantile=None, min_value=None, cmap='bwr')[source]#

Convert a 3D gene expression array to a Volume actor.

The isosurface threshold can be set as a hard value or as a percentile of the expression data.

Parameters:

  • griddata (ndarray[tuple[Any, ...], dtype[TypeVar(_ScalarT, bound= generic)]]) – 3D array with gene expression data.

  • min_quantile (float | None) – Percentile threshold for isosurface extraction.

  • min_value (float | None) – Hard value threshold for isosurface extraction.

  • cmap (str) – Colormap name. Default "bwr".

Return type:

Volume