How to create UMAP embeddings from indexed BED files
To create UMAP embeddings from indexed BED files in the BEDbase database, you can use the bedboss download-umap command.
This command generates UMAP embeddings for visualizing the relationships between different BED files based on their genomic regions.
Key features of the bedboss download-umap command:
- User can specify the number of dimensions to return (2 or 3).
- If user selected 2 dimensions, script can generate a umap plot.
- If user choose to generate a plot, user can specify what metadata column to color the points by.
Example
Let's say we want to create a 2D UMAP embedding of the top 10 assays and top 10 cell lines from our BEDbase database, and generate a plot colored by assay type. We can run the following command:
bedboss download-umap --config <path_to_bedbase_config> \
--output-file umap_embeddings.csv \
--n-components 2 --plot-name umap_plot.png \
--plot-label assay --top-assays 10 --top-cell-lines 10
Full bedboss download-umap help"
bedboss download-umap --help
Usage: bedboss download-umap [OPTIONS]
Download UMAP
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * --config TEXT Path to the bedbase config file [default: None] [required] │
│ * --output-file TEXT Path to the output file where UMAP embeddings will be saved [default: None] [required] │
│ --n-components INTEGER Number of UMAP components [default: 3] │
│ --plot-name TEXT Name of the plot file [default: None] │
│ --plot-label TEXT Label for the plot [default: None] │
│ --top-assays INTEGER Number of top assays to include [default: 15] │
│ --top-cell-lines INTEGER Number of top cell lines to include [default: 15] │
│ --help Show this message and exit. │
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