Added 4 Sphinx gallery python tutorials#43
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June 23, 2025 13:49
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Thank you. Are you sure the PNG static files should be versioned? |
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@iosonofabio Hi Fabio, yes these PNG files in _static folder are manually added for gallery thumbnails and should be versioned :3 |
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I disagree
…On Mon, Jun 23, 2025, at 16:02, Amber-Xu914 wrote:
*Amber-Xu914* left a comment (fabilab/cell_atlas_approximations_API#43)
<#43 (comment)>
@iosonofabio <https://github.com/iosonofabio> Hi Fabio, yes these PNG
files in _static folder are manually added for gallery thumbnails and
should be versioned :3
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iosonofabio
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Jun 23, 2025
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Thanks for the pr. I left a few dozen comments about specific points.
I'm not sure the logos for each tutorial make much sense. Maybe using a dynamic plot from the tutorial itself is more informative?
| # Files generated during package build and CMD check, unnecessary for the package | ||
| atlasapprox.Rcheck/ | ||
| .Rhistory | ||
| .RData No newline at end of file |
| ========== | ||
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| 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 |
| sns.heatmap(expression, ax=ax) | ||
| fig.tight_layout() | ||
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| # sphinx_gallery_thumbnail_path = '_static/quickstart.png' No newline at end of file |
| # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ||
| # It's recommended to use a virtual environment to manage dependencies. Run the following command: | ||
| # | ||
| # ``python -m venv venv`` |
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Actually people typically put it into .venv - with a dot
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| # List available organisms | ||
| available_organisms = api.organisms() | ||
| print(available_organisms) |
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Why not just printing the API call directly?
| # %% | ||
| # Visualizing the data | ||
| # -------------------- | ||
| # Visualization reveals patterns hidden by raw numbers. Organs vary in sampled cell totals, so raw counts can be misleading—those with more samples may appear to have higher cell type numbers, even if the type is rare. |
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Please cut the first clause, it sounds condescending
| # %% | ||
| # The bar chart indicates macrophages are highly abundant in the lung, comprising | ||
| # nearly 35% of sampled cells. This suggests the lung is a primary site for | ||
| # macrophage activity, while other organs like liver and bladder show moderate |
| # nearly 35% of sampled cells. This suggests the lung is a primary site for | ||
| # macrophage activity, while other organs like liver and bladder show moderate | ||
| # proportions, and many, such as pancreas and colon, exhibit minimal presence. | ||
| # The variation highlights the diverse roles macrophages play across the body's tissues. |
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Not sure what this means
| # | ||
| # For more detailed information, please refer to the `official documentation <https://atlasapprox.readthedocs.io/en/latest/python/index.html>`_. | ||
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| # sphinx_gallery_thumbnail_path = '_static/cell_type.png' No newline at end of file |
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Please let's make these dynamic
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Don't you already have a section on marker genes above? It feels like this tutorial might be redundant?
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Hi Fabio,
As discussed in the previous lab meeting, I’ve added 4 new tabs to the Sphinx gallery following the existing infrastructure. The source .py files are located in docs/gallery/python.
The gallery includes four Python tutorials now:
• Quickstart
• Beginner guide
• Explore average expression
• Explore cell type
• Explore marker genes
I followed Sphinx documentation conventions for file naming with numbered prefixes to ensure proper display order.
To generate the Sphinx gallery, simply run the make html command.
Please let me know if you have any feedback or require further adjustments.