HESTData: provide util to map ensemble ID to gene name

src/hest/HESTData.py

@@ -1244,6 +1244,37 @@ def unify_gene_names(adata: sc.AnnData, species="human", drop=False) -> sc.AnnDa
 
     return adata
 
+def ensembleID_to_gene(st: HESTData, filter_na: bool = False) -> HESTData:
+    """
+    Converts ensemble gene IDs of a HESTData object using Biomart annosations
+
+    Args: 
+        st (HESTData): HESTData object
+
+    Returns: 
+        HESTData: HESTData object with gene names instead of ensemble gene IDs
+    """
+    import scanpy as sc
+    species = st.meta['species']
+    org = "hsapiens" if species == "Homo sapiens" else "mmusculus"
+
+    annotations = sc.queries.biomart_annotations(org=org,attrs=['ensembl_gene_id', 'external_gene_name'], use_cache=True)
+    ensembl_to_gene_name = dict(zip(annotations['ensembl_gene_id'], annotations['external_gene_name']))
+
+
+    st.adata.var['gene_name'] = st.adata.var_names.map(ensembl_to_gene_name, na_action=None)
+
+    if filter_na: 
+        st.adata.var_names = st.adata.var['gene_name'].fillna('')
+    else: 
+        st.adata.var['gene_name'] = st.adata.var['gene_name'].where(st.adata.var['gene_name'].notna(), st.adata.var_names)
+
+    valid_genes = st.adata.var['gene_name'].notna()
+    st.adata = st.adata[:, valid_genes]
+
+    return st
+
+
 def save_spatial_plot(adata: sc.AnnData, save_path: str, name: str='', key='total_counts', pl_kwargs={}):
     """Save the spatial plot from that sc.AnnData
 

src/hest/__init__.py

@@ -3,7 +3,7 @@
 from .utils import tiff_save, find_pixel_size_from_spot_coords, write_10X_h5, get_k_genes, SpotPacking
 from .autoalign import autoalign_visium
 from .readers import *
-from .HESTData import HESTData, read_HESTData, load_hest, iter_hest
+from .HESTData import HESTData, read_HESTData, load_hest, iter_hest, ensembleID_to_gene
 from .segmentation.cell_segmenters import segment_cellvit
 
 __all__ = [
@@ -20,5 +20,6 @@
     'autoalign_visium',
     'write_10X_h5',
     'HESTData',
-    'segment_cellvit'
+    'segment_cellvit', 
+    'ensembleID_to_gene'
 ]