# Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""
Gene expressions
~~~~~~~~~~~~~~~~

``siibra`` can query gene expression data from the Allen brain atlas. The gene
expressions are linked to atlas regions by coordinates of their probes in MNI
space. When querying feature by a region,  ``siibra`` automatically builds a
region mask to filter the probes.

.. hint::
    This feature is used by the `JuGEx toolbox
    <https://github.com/FZJ-INM1-BDA/siibra-jugex>`_, which provides an
    implementation for differential gene expression analysis between two
    different brain regions as proposed by Bludau et al.
"""

# %%
import siibra
from nilearn import plotting
# sphinx_gallery_failing_thumbnail = False

# %%
# We select a brain region and query for expression levels of GABARAPL2.
region = siibra.get_region("julich 2.9", "V1")
features = siibra.features.get(
    region, siibra.features.molecular.GeneExpressions,
    gene=siibra.vocabularies.GENE_NAMES.GABARAPL2
)
print(features[0])
# Take a peek at how the data looks
features[0].data.head()

# %%
# Since gene expressions are spatial features,
# let's check the reference space of the results.
space = features[0].anchor.space
print(space)

# %%
# Plot the locations of the probes that were found, together with the region
# mask of V1.
all_coords = [p.coordinate for p in features[0].anchor.location]
mask = region.get_regional_mask(space)
display = plotting.plot_roi(mask.fetch())
display.add_markers(all_coords, marker_size=5)