Added 4 Sphinx gallery python tutorials

.gitignore

@@ -149,4 +149,11 @@ dmypy.json
 # Files generated during package build and CMD check, unnecessary for the package
 atlasapprox.Rcheck/
 .Rhistory
-.RData
+.RData
+
+# sphinx gallery src
+docs/source/_build
+docs/source/python/gallery
+
+# OS system file
+**/.DS_Store

docs/gallery/python/quickstart.py → docs/gallery/python/0_quickstart.py

@@ -2,7 +2,8 @@
 Quickstart
 ==========
 
-This example shows a quick and easy example of how to use atlasapprox to get and plot the expression of some gees in a specific organ of a specific organism.
+This example shows a quick and easy example of how to use atlasapprox to get and plot the expression of some gees in a
+specific organ of a specific organism.
 """
 
 import matplotlib.pyplot as plt
@@ -19,3 +20,5 @@
 fig, ax = plt.subplots(figsize=(7, 4))
 sns.heatmap(expression, ax=ax)
 fig.tight_layout()
+
+# sphinx_gallery_thumbnail_path = '_static/quickstart.png'

docs/gallery/python/1_beginner_guide.py

@@ -0,0 +1,100 @@
+"""
+.. _beginner-guide:
+
+Beginner guide
+==============
+
+The `atlasapprox <https://atlasapprox.readthedocs.io/en/latest/index.html>`_ API provides access to approximated
+cell atlas data from 30 species, including both animals and plants. You can explore data from species such as *Homo sapiens* (humans), *Mus musculus* (mice), *Arabidopsis thaliana* (thale cress), and *Zea mays* (corn).
+This guide walks you through installing the package, setting up the API, and running basic queries with simple examples.
+"""
+
+# %%
+# Setting up a virtual environment (optional)
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+# It's recommended to use a virtual environment to manage dependencies. Run the following command:
+#
+#     ``python -m venv venv``
+#
+# Activate the environment using the appropriate command for your operating system:
+#
+# For macOS/Linux:
+#     ``source venv/bin/activate``
+#
+# For Windows:
+#     ``venv\Scripts\activate``
+
+# %%
+# Installing required packages
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+# Install the ``atlasapprox`` package along with libraries needed for data visualization using *pip*:
+#
+# ``pip install atlasapprox matplotlib seaborn numpy pandas``
+#
+# These packages will be used throughout the tutorials.
+
+# %%
+# Then, import required libraries and instantiate the ``API`` object:
+
+import atlasapprox
+
+api = atlasapprox.API()
+
+# %%
+# Querying available data
+# ^^^^^^^^^^^^^^^^^^^^^^^
+# Explore available organisms, organs, and cell types using the following methods:
+
+# %%
+
+# List available organisms
+available_organisms = api.organisms()
+print(available_organisms)
+
+# %%
+
+# List available organs for humans
+available_organs = api.organs(organism="h_sapiens")
+print(available_organs)
+
+# %%
+
+# List available cell types in the human lung
+available_celltypes = api.celltypes(organism="h_sapiens", organ="lung")
+print(available_celltypes)
+
+
+# %%
+# Exploring average gene expression
+# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+# The ``average`` method retrieves gene expression levels for selected genes in a specific organ of an organism.
+#
+# The following example shows how to examine the average expression of five genes
+# (*COL13A1*, *COL14A1*, *TGFBI*, *PDGFRA*, *GZMA*) in the human lung:
+
+avg_gene_expr_lung = api.average(
+    organism = "h_sapiens",
+    organ = "lung",
+    features = ["COL13A1", "COL14A1", "TGFBI", "PDGFRA", "GZMA"],
+    measurement_type = "gene_expression"
+)
+
+# Display the result
+avg_gene_expr_lung
+
+# %%
+# Understanding the output
+# ------------------------
+# The ``average`` method returns a **pandas.DataFrame** where:
+#
+# - Rows represent genes.
+# - Columns represent cell types.
+# - Values show average gene expression in counts per ten thousand (cptt).
+
+# %%
+# Conclusion
+# ^^^^^^^^^^
+# This guide covers setup and basic data querying. For more detailed
+# information, refer to the official `documentation <https://atlasapprox.readthedocs.io/en/latest/python/index.html>`_.
+
+# sphinx_gallery_thumbnail_path = '_static/beginner_guide.png'