read function and fixes (#1034)

fix req, modified datasets, added read_visium
scverse · Feb 11, 2020 · 4bf1532 · 4bf1532
1 parent 09b9856
commit 4bf1532
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diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-anndata>=0.6.22.post1
+anndata>=0.7
 # matplotlib 3.1 causes an error in 3d scatter plots. Once solved the dependency can be updated (https://github.com/matplotlib/matplotlib/issues/14298)
 matplotlib==3.0.*
 pandas>=0.21

diff --git a/scanpy/__init__.py b/scanpy/__init__.py
@@ -40,7 +40,7 @@
 
 from anndata import AnnData
 from anndata import read_h5ad, read_csv, read_excel, read_hdf, read_loom, read_mtx, read_text, read_umi_tools
-from .readwrite import read, read_10x_h5, read_10x_mtx, write
+from .readwrite import read, read_10x_h5, read_10x_mtx, write, read_visium
 from .neighbors import Neighbors
 
 set_figure_params = settings.set_figure_params

diff --git a/scanpy/datasets/__init__.py b/scanpy/datasets/__init__.py
@@ -12,7 +12,7 @@
 from .. import logging as logg, _utils
 from .._compat import Literal
 from .._settings import settings
-from ..readwrite import read, read_10x_h5
+from ..readwrite import read, read_10x_h5, read_visium
 from ._ebi_expression_atlas import ebi_expression_atlas
 
 
@@ -366,29 +366,7 @@ def visium_sge(
         else:
             _utils.check_presence_download(filename=files[f], backup_url=backup_urls[f])
 
-    # read h5 file
-    adata = read_10x_h5(files['counts'])
-    adata.var_names_make_unique()
-
-    # read images
-    # imread only accepts strings, not Path objects
-    adata.uns['images'] = dict(
-        hires=imread(str(files['hires_image'])),
-        lowres=imread(str(files['lowres_image'])),
-    )
-
-    # read json scalefactors
-    adata.uns['scalefactors'] = json.loads(files['scalefactors_json_file'].read_bytes())
-
-    # read coordinates
-    positions = pd.read_csv(
-        settings.datasetdir / 'spatial/tissue_positions_list.csv', header=None
-    )
-    positions.columns = ['index', '0', '1', '2', 'X2_coord', 'X1_coord']
-    positions.index = positions['index']
-
-    positions = positions.join(adata.obs, how='right')
-
-    adata.obsm['X_spatial'] = positions[['X1_coord', 'X2_coord',]].to_numpy()
+    adata = read_visium(files['counts'])
 
     return adata
+