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.

Note

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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