Update folder and file descriptions for updated visuals.
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README.md
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@@ -29,6 +29,7 @@ The `notebooks` folder contains
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- `ToL_catalog_EDA.py`: py file paired to `ToL_catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
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- `ToL_predicted-catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `predicted-catalog.csv`. To be updated as `predicted-catalog.csv` is updated, i.e., as the dataset is updated.
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- `ToL_predicted-catalog_EDA.py`: py file paired to `ToL_predicted-catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
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- `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `catalog-v1-dev.csv`, generates `taxa_counts.csv`.
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- `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of visualizations in `visuals` folder and some histograms. The treemaps produced in the notebook are interactive.
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### Visuals
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Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M.
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There is also one for just the iNat21 data included.
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- `ToL_catalog_EDA.py`: py file paired to `ToL_catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
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- `ToL_predicted-catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `predicted-catalog.csv`. To be updated as `predicted-catalog.csv` is updated, i.e., as the dataset is updated.
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- `ToL_predicted-catalog_EDA.py`: py file paired to `ToL_predicted-catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
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- `BioCLIP_taxa_viz.ipynb`: generates data visualizations, in particular, the generation of treemaps in `visuals` folder; also includes a histogram of kingdoms. The treemaps produced in the notebook are interactive and `HTML` interactive versions can also be found in [`visuals`](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/visuals).
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- `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `catalog-v1-dev.csv`, generates `taxa_counts.csv`.
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- `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of visualizations in `visuals` folder and some histograms. The treemaps produced in the notebook are interactive.
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### Visuals
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Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M.
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- `category-v1-visuals`: visualizations made for the original `catalog-v1-dev.csv` using `BioCLIP_taxa_viz_bySource.ipynb`.
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There is also one for just the iNat21 data included.
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- `kingdom_ToL_tree.html`: interactive treemap from `kingdom` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.
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- `kingdom_ToL_tree.pdf`: static treemap from `kingdom` to `family`to demonstrate the distribution of the data. 2:1 aspect ratio.
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- `phyla_ToL_tree.html`: interactive treemap from `phylum` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.
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- `kingdom_ToL_tree.pdf`: static treemap from `phylum` to `family` to demonstrate the distribution of the data. 2:1 aspect ratio.
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